There's a step by step Tutorial for this in the FAQ

Q: How can I delete samples stored in the Internal Memory (like stock sounds or whatever)?
A: Well, actually you really can't just delete them. But what you can do is, overwrite them. At least in the AKAI OS or JJ-OS 1. In OS 2, the internal memory doesn't seem to be accessible any longer (at least in version 1.18). So, what you need to do is this:

1. Turn Off Auto-Load for Internal Memory.
2. Restart the MPC.
3. Record some silence. 1 second is enough.
4. Enter Trim Edit and change it's length from whatever it is to 'End: 00000001', so that you just have the smallest possible sample length. Press Edit [F6] and discard the rest.
5. Assign that Sample in Program Edit
6. Now, go to Save Menu and select 'Save: ALL PROGRAMS' and select the program you put that super small sample in - it's called 'Program01' by default.
7. Press [Do It]. The following screen says: "This will erase all Programs and Samples in the internal flash memory". Press [Do It]. Done. At least it should be by now, but...
8. If you're internal flash memory was full before, you probably can't save that program with the sample. It needs 10 KB of free memory at least to be able to save.
9. If it didn't work, you have to load a program from the Internal Memory, with samples.
10. Go to trim, and change the length of the samples just as in step 4) and discard the rest.
11. Enter Save Menu again and save that exact Program, overwriting the old one. This should gain you the amount of free memory needed to save the other program.
12. Now repeat Steps 6 and 7 and all the Internal Memory should be garbage free by now!