Different IOS-XE versions have different ways of storing files. Cleaning them "manually" does not take away the gunk. It does not scratch the surface.
The most effective way is to perform a factory reset (command: factory-reset all) and will completely wipe everything (including different flash partitions). The switch will boot into ROMMON and the only way to put the firmware back in is to do an emergency-install (command: emergency-install usbflash0:filename.bin).