Hi, is it possible to tap the small holes in the CNC machined part with M3 threads?

Yes, it is OK to tap the holes with M3 threads.

For threads machining/tapping processing, the 2D drawing with annotated thread details (such as positions of the threaded holes, thread type, size, pitch etc...) are required.

So, please select "Threads-Yes" when ordering and submit your 2D annotated drawing together.