Cutting carbon brushes should be avoided as it's too risky. The best option is to sand or file brushes down carefully a bit at a time (using a fine a sand paper or a file) until they fit the desired brush holder of your machine.
Here at Top Deals Online, we have a range of "generic" brushes that can be modified like this to suit your application, along with specific types to fit the model of your power tool.
There is no need to bed in brushes, as once installed they should be up and running immediately, with no need to wear them in at all.