Use the side snips like Jonyjoe says, and instead of dremel, lay a sheet of sandpaper flat and rub the cell on that instead. Filings will be hard to get under the cap that way.
Also, unless you absolutely need a smooth surface, it's not idea to remove all the way down as most cell casings are nickel plated steel. If you remove the nickel plating, you are exposing iron to the air which can then rust. This is more of an issue on the Neg end than the Pos as the Neg end is directly the cell body, the Pos end is separate.
If you plan on soldering the cells later, go ahead and put some solder on them to cover the scratched area. Or put a little grease to keep the moisture off. Then clean with alcohol just before soldering them during assembly. This will keep it protected. This would be like petroleum jelly or something like that, something easily cleaned off. This is only if the cell will be sitting for a long while before you can get to them.
If you plan on spot welding them later, don't even worry about sanding the tabs down. And in fact, don't pull the tabs off at all, just snip closs to the cell and leave the original tab still spot welded. It's easier to spot weld nickel strip to nickel strip than to the cell casing, plus you don't put no where near as much heat into the cell that way.
And, it's also possible to just solder directly to this strip as well. Again, it'll drastically reduce the amount of heat that is put into the cell.
