Upgrading the Kernel is one of the steepest learning curves in Linux. It helps to have a guru on hand while you do this and also to read everything there is on the process... and I do mean EVERYTHING.
You can erase the directories the usual way
but you must be root.
#rm -d <directory>
Make sure you are not erasing the directories controlling your active Kernel. Remember to also remove any bootloader references as well.
I suspect you'll have trouble with the 2.6 kernel as well... the process is similar but there are more fiddly bits.
When in trouble... read the documentation. In this case:
this will tell all about removing the dircetory.