[Terry Capps]

There is a fairly simple way to do what you want.

1. Select the top surface of the roof and duplicate it.
2. Hide the roof object underneath that surface.
3. Select the duplicated surface as an OBJECT
4. Activate Tools, Knife, and then click on "Set Knife".
5. Un-select the duplicated surface and then select the chimney.
6. In the Knife Tool, click on "Cut away object", "Delete Knife", and then "Slice".
7. Select the lower portion of the slice chimney (it may already be selected) and delete it.
8. Unhide the roof (that you hid in step 2.