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.
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 one 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.
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:
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.