Take a look at the CISCO-FLASH-MIB to copy and delete files with snmp.
To delete a file called "isakmp_staticroute_eem.tcl" on flash:
#ciscoFlashMiscOP branch to call out file to delete, createAndGo
[dafrey@HammerHead TC$ snmpset -v 2c -c private 192.168.0.1 ciscoFlashMiscOpCommand.101 i 3 \ ciscoFlashMiscOpDestinationName.101 s isakmp_staticroute_eem.tcl \
ciscoFlashMiscOpEntryStatus.101 i 4
CISCO-FLASH-MIB::ciscoFlashMiscOpCommand.101 = INTEGER: delete(3)
CISCO-FLASH-MIB::ciscoFlashMiscOpDestinationName.101 = STRING: isakmp_staticroute_eem.tcl
CISCO-FLASH-MIB::ciscoFlashMiscOpEntryStatus.101 = INTEGER: createAndGo(4)
#Verify file is removed
[dafrey@HammerHead TCL]$ snmpwalk -v 2c -c private 192.168.0.1 ciscoFlashMiscOpTable
CISCO-FLASH-MIB::ciscoFlashMiscOpCommand.101 = INTEGER: delete(3)
CISCO-FLASH-MIB::ciscoFlashMiscOpDestinationName.101 = STRING: isakmp_staticroute_eem.tcl
CISCO-FLASH-MIB::ciscoFlashMiscOpStatus.101 = INTEGER: miscOpOperationSuccess(2)
CISCO-FLASH-MIB::ciscoFlashMiscOpNotifyOnCompletion.101 = INTEGER: false(2)
CISCO-FLASH-MIB::ciscoFlashMiscOpTime.101 = Timeticks: (200) 0:00:02.00
CISCO-FLASH-MIB::ciscoFlashMiscOpEntryStatus.101 = INTEGER: active(1)
#destroy row
[dafrey@HammerHead TCL]$ snmpset -v 2c -c private 192.168.0.1 ciscoFlashMiscOpEntryStatus.101 i 6
CISCO-FLASH-MIB::ciscoFlashMiscOpEntryStatus.101 = INTEGER: destroy(6)