Basically what i had in mind was a way to target a familiar with Anthropomorphic animal so that he can manipulate tools and speak, but since a familiar becomes a magical beast, it shouldn't be posible.
Is there a way around this?
All you need to do is cast the spell on your own familiar. Familiars, from master level 1, have an ability that has you covered:
Share Spells: The wizard may cast a spell with a target of “You” on his familiar (as a touch spell) instead of on himself. A wizard may cast spells on his familiar even if the spells do not normally affect creatures of the familiar's type (magical beast).
Emphasis mine. This clause is usually used to allow buffs to work on familiars that usually only work on humanoids, but it works just as well with buffs that usually only work on animals. Note that you can save a spell level and accomplish similar results with the Alter Self spell, though that one won't allow it to speak a language unless it has one to use, so if planning to do that version with any regularity, you'll want a thrush or raven as the base familiar.