I have a very peculiar situation. I installed a piece of software by building it from source. I used "make install" from the folder that I downloaded it into (on my desktop). Later on, after not using it for a while, I decided I don't need the folder on my desktop and shift-deleted it. Most files in that folder were deleted, but some of them cannot. It says I have no permissions to do it.

What I am assuming is that those files are used by the kernel, because the software was built from source. Is this correct, and if so, how can I delete them? Can I boot in another kernel or do something like Windows's safe mode?