The "make install" installs most files in /usr/lib/vlc and /usr/include/vlc (or /usr/local/lib/vlc if you have choosen another prefix) and the binaries in /usr/bin/ and some localization files in /usr/share.
If you want only to "clean" your old installation to avoid problems when installing a new version of vlc it is enough to erase /usr/lib/vlc:
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rm -rf /usr/lib/vlc
rm -rf /usr/include/vlc
If you don't do this and if you install a new vlc over the old one, they may indeed still be old non-erased plugins in /usr/lib/vlc which may create problems. Also the header files in /usr/include/vlc may create problems but only if you compile later things against libvlc (I believe).
If you are very worried about "clean" and "proper" installations and "uninstallations" then you should compile vlc with some prefix such as: "--prefix=/usr/VLC" and then simply add /usr/VLC/bin to your PATH after installation. Later it will be enough to simply erase the folder:
in order to "uninstall" everything from vlc.
If you install vlc in a standard tree, such as /usr or /usr/local then it is more difficult to "uninstall" everything.