'make clean' should clean up the directory a little. But if you don't plan on looking at the source much after the intial install, in most cases you can just remove the directory. Usually a good way to check is to see if the file installed itself to a default directory ('whereis program', see if its in /usr/bin, /usr/local/bin, etc.) or you can always skim the Makefile. The safest way would be to move the directory with all its files to a different location (or just rename it). this way, if the program still runs, you're pretty safe in removing it.
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