Import .flac to after effects cs6
Sadly Adobe doesn't support FLAC in any of their video products. The only Adobe product that supports it so far is Audition.

Though there is this great and open source plugin that works just fine with CS6 even though it was made for CS5. Plugins made for CS5 are usually compatible with CS6 and CC.

For CS4 there is a 32bit version of the same plugin: http://valion.net/flacimporter/