You should be able to delete the files in Storage CLI
Are you running in C mode or 7 mode ?
7 mode
1) Swith to diag mode
filer2> priv set diag
Warning: These diagnostic commands are for use by NetApp
personnel only.
2) list the files in the volume using ls command . You need to give the complete path /vol/dir1/dir2/dir3/dir4/dir5/...
filer2>ls /vol/vol_test/
.
..
test3.txt
test.exe
test2.txt
filer2>
3)Remove the file by using rm commnad
filer2*> ls /vol/vol_test/
.
..
test3.txt
test.txt
123.exe
test2.txt
filer2*> rm /vol/vol_test/123.exe
filer2*> ls /vol/vol_test/
.
..
test3.txt
test.txt
test2.txt
filer2*> priv set
filer2>
For C mode
You need to run the same node level commands in the node where the volume is created