You don't mention if you have peripheral relatives. Did you enter siblings of ancestors? Other spouses of ancestors who are not your ancestor? Spouses of siblings? Children of Siblings?
If there no other ties to "your tree", I take it that you have detached him from being your ancestor?
You delete groups of people in FTM by using Publish > Charts. You can delete people in most charts by right-clicking in the blank space in the report, and select "Delete everyone in this chart". (I suggest Export everyone in this chart, then delete everyone in this chart. This will leave a record of who you deleted.) You can also select certain persons in a chart and export and/or delete "only selected persons" in a chart.
There are probably two charts you may want to use:
1) Ancestral Chart. Select the bad apple ancestor and make the number of generations inclusive enough to include all persons you want. This will NOT delete any peripheral relatives and will only delete "preferred parents" of each ancestor.
2) Extended Family Chart. Select the "bad apple" ancestor. Since you have apparently already detached them from being your ancestor:
1) Make the number of generations to include all you want to delete
2) Uncheck the box in the right panel to "include everyone" in your file.
3) Right-click > Export everyone in this chart (This just documents who you will be deleting)
4) Right-click > Delete everyone in this chart.
This should include all peripheral relatives - prior and subsequent spouses of ancestors, step-children, siblings, siblings' spouses, nieces and nephews of ancestors, etc.