Only few Cherry keycaps are two-shot moulded, so you'll need patience and luck finding any. Plastics seem to be identical, though, so you'll get POM or PBT depending on keycap colour.
Filco's keys are taller than Cherry's, so I wouldn't recommend replacing single keys in the alphanumeric area. Replacing everything except shift, return, etc. shouldn't be much of a problem, though, as this doesn't feel extremely weird when typing.
-huha