You need to do it recursively, take a look (it is just an example):
sub RecursiveDeleteByExtension(byval strDirectory,strExtensionsToDelete)
DIM objFolder, objSubFolder, objFile
DIM strExt
set objFolder = objFSO.GetFolder(strDirectory)
for each objFile in objFolder.Files
for each strExt in SPLIT(UCASE(strExtensionsToDelete),",")
if RIGHT(UCASE(objFile.Path),LEN(strExt)+1) = "." & strExt then
wscript.echo "Deleting:" & objFile.Path
objFile.Delete
exit for
end if
next
next
for each objSubFolder in objFolder.SubFolders
RecursiveDeleteByExtension objSubFolder.Path,strExtensionsToDelete
next
end sub