In all the years of building any type of wheels with the spokes being too long I've always filed them flush with a 1/4"- 3/8" square file. This way the user has complete control of the tool and leads to a more professional finish plus no damage or scoring to the rim. This method is usually required on the older single skin rim when it is very difficult to always get the length correct due to the new or old spokes not always being the exact measurement.
Ofcourse getting the length correct on the outset must be the answer but it does'nt always work that way.
Doug Smith
North Dorest
UK