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Here's a quick little script to clean the default mail accounts of mail on cPanel servers.  Note that this only helps if you have already disabled the catchalls.

#!/bin/bash
###############################################
# CLEAN MAIL #
# v0.1 #
# #
# Cleans the mail from default accounts based #
# on cPanel usernames. Create a file in /root #
# called 'doit'. Add one cPanel username per #
# line. That should do nicely. Oh, this will #
# take a while, so run the sucker in screen, #
# mkay, Batman? #
###############################################

# Some dedis have LS_OPTIONS include -a...
# that would be bad for this script.
# so, we reset it.
LS_OPTIONS='-A'

# start the loop...
for i in `cat /root/doit`
do
# Delete from the new folder.
cd /home/$i/mail/new
# can't rm if there's too many, and by using
# an ls and awk, we avoid another loop.
ls -l | awk '{print "rm -fv "$9}'|bash
# Delete from the cur folder.
cd /home/$i/mail/cur
# Comment repetition carefully avoided, here
ls -l | awk '{print "rm -fv "$9}'|bash
done
# NINJAMOJO!

It's simple. Get a list of cPanel usernames, one per line, create a file in /root called 'doit', and slap the usernames in there.  Then, 'bash cleanmail'.