I would assume that by your observations of the sub-directories that you are running Squid as your web cache server. Squid and your web server have nothing in common unless you are proxying inbound connections for you internal web server, but that is a whole 'nother issue....
Really the easiest and quickest way to clear your cache in Squid is to note the user/group that owns /webcache along with permissions on the directory - then 'rm -r /webcache' (this is DEFINATELY assuming you only have the cache directories below /webcache and nothing else. If there is other stuff, you will have to delete each individual directory...) Once you have deleted all the old cache directories, recreate the 'webcache' directory with the same owner, group and permissions as previous, then launch 'squid -z' which will recreate the cache directory structure..
Hope this helps,
Paul