Delete network folders?

I am working with a friend (just being an extra hand) on cleaning up a network he just took over to manage. I don't know much but am trying to help, sorry if I don't use correct terminology.
He is trying to get rid of old folders on the network. Most of the folders we are able to delete but there are some that are giving us problems. The network is on/uses NT4.0. He has full control permissions and took ownership of the folders. Everything deletes in the folders but MS-Dos Prompt. We get an error that says Access denied, make sure this program is not in use or write protected. Since we can not get rid of that program the folder doesn't go away.
Not really sure what the problem is but am certain my bud would be glad if I could come up with an answer.
Thanks for any help.

malo_4