[quote]It would be nice if I could just delete the Trees in place without creating new files.[/quote]Actually it probably would not, as the resulting file would take more space than necessary as it would not ‘free’ the gap left by the removed TTree (and thus your next question would be 'how do I compact my sparsely filled ROOT file).
Alternatively you may not (if the TTree that you do not need are small) have to store them in the first place; if they fit in memory call mytemptree->StDirectory(0);
Cheers,
Philippe.