While technically this is possible, I would caution trying to do this in many cases.  With Isilon file clones each file must be cloned individually.  So it could be scripted through the CLI (and possibly the API), I would only do this on directory structures that have a few files as the time to clone a large number of files will most likely not meet the customer's expectations.
I have a customer who is using the NetApp FlexClone software and wants to do this on Isilon.  Is this possible using the file clone feature in 7.0?
File Clones to clone a directory