Is there any way for law enforcement to hunt down a wanted adept who can change his face at will? I have a player with a rather large bounty on his head, and a very powerful enemy (yeah, he made more than a couple bad decisions), but he's able to simply integrate into society like nothing ever happened because of facial sculpt and melanin control. Is there some logical way to put heat on him from the trouble he caused?
Note: I haven't played SR3 much, my experience is more with SR4.
Also, note: This situation can easily turn into an arms race. People have different reasons for playing untouchable characters (grossly simplified: from inexperience to inferiority complex). Take into consideration whether it will make the game more fun for your group when you start bringing out the big guns on this. If this overpowered char is ruining other peoples' fun, it might be a better solution to discuss it in the group and find another character for him.
There is a bunch of different things that can be tracked except for looks. Since you said that he has made a very powerful enemy, this opposition should be building up a budget over time roughly proportionate to the anger and time that has passed. At some point the expertise of the "case worker" will be sufficient to make trouble for your player's character.
Assuming the enemy is sufficiently organized and antagonized, he will be building a profile, collecting any hints until a pattern emerges.
People keeping an eye on the shadows will be aware of your player's character through tales of his feats. The opposition will learn about his abilities and take them into account.
If he is actively working to keep a low-profile, you may show him the downside of that: Being a nobody, job offers will be worse, pay will be worse for the same job, new contacts are less willing to go out of their way to help him. People will be more likely to consider him an easy scapegoat.
He is probably not working alone, and thus inquiries can be made about his associates. Especially, if he works with specific contacts regularly at some point somebody will be made an offer that cannot be refused. This might turn into a mole or a setup.
Again, if he doesn't do associates, this will lead to situations where he does need help and the counter-party has little to no interest to cover him.
He might have hobbies like watching games of a specific team or hanging at a particular pub. Different sightings of the character will be used to narrow down his area of operation and home turf. Again, this might lead to further information sources, and opportunities to start shadowing him. If a specific location can be tied to him, it is also very easy to install some micro cameras and microphones to gather more information on him, and inconspicuously watch for his appearance.
Speech patterns, vocabulary, gait, and other mannerisms might be collected and used to build a person recognizer specifically matched to him. If he is not aware of such an effort, he will not be trying to work against it, making it more likely to succeed. This would require a significant amount of training data, so he would have to been pretty bold about showing up on cameras and such.
It might be possible to follow his vehicle or his phone. He might have a piece of favorite clothing that is distinct enough to give him away. It might be possible to attach a tracking device in some fashion.
I cannot find the particular rules on this right now, but at least magical attacks on others should leave an astral signature remaining for power level hours after the application (in SR4). Should a magician search the murder scene soon enough, he might be able to extract an astral signature, which he can recognize when he sees it. Magical active people are fairly rare, which might make him stick out on another occasion as well.
Law-Enforcement might create a psychological profile, giving e.g. hints as to what might lure your player's character out of hiding, allowing for a trap set specifically for him.
Perhaps he has an affinity to a certain type of job or target, it becomes known that he supports a certain minority's causes, or some of his goals become known.
Once the identity of the player's character is established, it might be beneficial to dig through his past. Shadowrunners don't appear out of thin air. They have credit histories, criminal records, former neighbors, family, loved ones, and old highschool friends. Some of them might be sufficiently important for him to be used to paint a thinly veiled threat, or alternatively can be social-engineered to reveal more useful information about the target.¹ – That is, unless his character did appear from thin air. ;)
Most of these techniques are pretty resource intensive and/or failure-prone. They are certainly not going to create a problem for him all the time, but when the time is right, somebody just might have all the pieces ready to pounce. It would also be very likely that several approaches are followed at the same time.
¹Thanks @TimothyAWiseman for the suggestion.
I am not expert in Shadowrun system, but I think some common ground GM "tactics" could help here. These are just general ideas - again I just barely know Shadowrun setting.
Being in a world with an advanced technology and magic altogether gives you some great leverages. You could, for example:
have him chased by some sort of special squad made by nanotechnology-enhanced agents that are able to analyze his DNA in some way, just find a way to explain how they collected a sample - and it's easy if he's actually making noise around
have him chased by an agent of some normal law enforcement corp, but this particolar agent could be some sort of magic-user and have something personal against him, or just being recruited and/or well-paid by this enemy of him to chase him and lock him down, and using magic you can stalk him in many ways - think about magical items, spell tracking his astral aura, or thinkgs like that
he could have some sort of home where he returns, or people that he sticks to (other players?), or material belongings (car? phone?) that can be tracked instead.
Two additional cents: remember that the entire point of playing an RPG is FUN, not players punishment or education. As a GM, you're not playing against your players, you're helping them to have FUN. So it's good to provide him with some challenge, and being hunted down it's a good start - but if he enjoys to get away with it, well, think about allowing it. Maybe make it hard, make him earn it with sweat and blood, but in the end he should be allowed to escape safely, again, IMHO.
I see a lot of great options already proposed in the other replies, but there's one that I don't seem to see in here at all.
Scent tracking. Granted, we the general populace know he's an adept and his opposition likely doesn't, but aside from scent glands(which would give an altered but still definite scent) or possibly clean metabolism (which sanitizes) if there's anything left behind they've had significant contact with, bring in the bloodhounds. I'd argue that those who pitched in for tailored pheromones would be even worse off, due to being engineered to spread their altered stink to a wider audience.
Send out an investigator who has an orientation system, coupled with a gas spectrometer and chemical analysis package wired in. A dog would be cheaper, but a (meta)human who can track without being so obvious might be more effective. Once they've started to nail down the trail, use that headware to inform head office or call in backup.
Keep in mind the security rating of the zone he's in as well. Anything with a rating of A or above (like most of downtown Seattle proper) has regular foot/bike/car patrols, and they also have security cameras at least every block maintaining solid views of the streets. Backtrack that person by clothing (and gait, like modern security does) and catch him between guises if he changes near the area or within the trackable timeframe.
Once your scent-snoop is on the scene, if it's fast enough, they may be able to start working to pin down where this guy has been going into hiding.
If you've exhausted the mundane means and magic has to come into play to deal with them, while their own innate talents don't (usually) leave an astral signature behind, any active weapon foci might. I've made sure to note down things like killing hands or distance strike as active magical effects that leave trails, even occasionally a boosted attribute because of the drain factor.
Have the DPI (or other local equivalent) recruit somebody skilled with the sympathetic magic. Go for a Symbolic linking(Src: SOTA 2064, p. 47), which can help them track down a target for who they have no name or directly-connected material link.
Facial Sculpt and Melanin Control do not to cover your identity
If your character stays away from places where IDs are needed he can use facial sculpt and melanin control to look like another person. But if IDs are needed you have to give away fingerprints and retina scans that are not changed by both adept powers. So if law enforcement finds fingerprints they can add those to their database. If the character veer walks through a checkpoint his IDs will be checked and he gets problems with police. His nemesis might have bribed or hacked inside those recordings and could get informations about his whereabouts.
Astral search, natural spirits and Detection spells
There are some ways to get the position from persons without needing to know their face and skill color. Especially if you get a fresh blood drop during a combat scene you could preserv this to search for your position later on. If a shaman would see the character and his asral aura he could use a city spirit with search power to find you in his domain. I would allow to find a facial sculpted person with detect person spells but the range is small (even for extended versions of the spell).
Shadowrun and realistic enemies
If law enforcement/corps would do everything to hunt criminals and SINners they could find everyone. But it is not in the interest of most corps to find everyone and for corporations like Lone Star it is not worth to put that much money into one simple criminal.
So if you bring down such search methods to your player you should justify this by his behavier. Did he kill the daughter of the CEO form Lone Star? Sure now they will put every Nuyen into the man hunt for the killers. But after how much money will a rival lone star manager use that information to get CEO himself - and end the man hunt?