How can I do a clean-up?
 

When I install a software from source, there are many (source, object,etc.) files that might be removed after the binary is ready.
How can I remove them?
(P.S. I tried 'make clean', but that destroyed the program.)

well you'd either just delete the entire source directory or not. erm.. i guess you could put the stuff back in a tar.bz2 or something if you think you might need it later. make clean won't stop the program working, only the uninstalled version in the source directories.

Do a clean-up
 

Actually, 'make clean' command ruined my xmms, and I had to recompile and install it.
On the other hand: I do not know if I have a 'source directory'.
If I simply use
./configure
make
make install
will the compiled binary files or other necessary files reside in the same directory where the source and object files can be found? If so, I cannot delete the source directory as it also contains the binaries.

...
 

If you want to remove files, that ./configure created, you just have to run 'make distclean' (it won't harm the sources)