The simplest step is to use paper that allows better penetration of ink or toner.
Much glossy preprinted stock lets the ink or toner sit on top of the surface where it is easily removed by scraping and/or bleaching.
A finely patterned background that will be damaged when any overprinting is removed is also a help.
Unfortunately, I expect that your cheques are printed for you by the bank.
Lasers printers are in general more permanent than inkjets as they are waterproof.
Some inkjet inks are water based and hence can be washed off, others are not.
an example below:
http://www.inkkeepers.com/product_details.asp?id=36900The only other way to go is to use colour printing.
Colour lasers print at higher temperatures than mono ones, they also put on 4 layers of toner, and some now use organic toners which include wax. all of these factors make it harder to remove the impression by scratching.
Or, you could print your cheques in a particular shade of green for example, which would be difficult to match or replicate, and would show up when processing.
Dye sublimation printers can be even more permanent, as they actually dye the paper, but they are generally expensive.
Dot matrix printers may be another option.