You have to either keep the complete template sequence in the PDB file, 
or modify the template PDB to remove the residues you don't want. An 

alignment that achieves what you want without modifying the PDB is:

      target: AAAAAAAAAAA-------AAAAAA
  template 1: BBBB-------BBBBBBBBBBBBB
  template 2: ZZZZZZZZZZZ-------ZZZZZZ

	Ben Webb, Modeller Caretaker

Is it algorithmically difficult to add a function that will select a range of residue in one template and Modeller will exclude them without touching the alignment? When having multiple templates and several unwanted regions this procedure becomes very tedious.