How can I trim a window stool (sill) without removing it. I need to cut it flush with the wall. it just needs to be straight.

 

In short, Very carefully!

Is there room to slip something in behind the tongue of the stool (inbetween the stool and the wall) so that the wall will be protected while you cut? If so, that would be an excellent idea. Sheetmetal, trim coil, even a scrap of heavy paper- anything would help keep you from knicking the wall.

I'd recommend you use a dovetail saw, since the handle is behind the teeth, it would allow you to saw without beating up your knuckles -or- the wall! Additionally, you could try a fine cut saw (a type of pull saw made by Shark Saw or Irwin). They are super sharp and since they cut on the pull stroke, you can often be far more precise with it. You'd be surprised how fast they cut.