Your best option is to Package your file with all fonts and images (via 'File - Package'). Then all used fonts and images will be on one folder. You could then effectively trash all other folders, getting rid of your mess. Besides you, likely only InDesign knows what you you used, so this is the way to do it. Here is how to Package in InDesign CS6:
I hope this helps.
Message was edited by: David Dilling (grammar)