Remove the bolts and bracket from your cooler and your motherboard, and thread the bolts all the way through your bracket, as shown above. The importance of this will be explained in a bit.
Now, using your bolt-cutter, or using a pliers' bolt cutter, cut a few threads above the lowest mark, we will use the file to trim it down tho the proper length. Once you've got them cut, use a pliers to hold the bolt in one hand, and then file down, rounding out the edges of the threads as you file it down to avoid any protruding pieces from catching the nut in the mounting bracket.
Once you've got it filed down to the desired length, and making sure all the burs and wide edges are filed down smooth and flush, then begin turning out the bolt by hand from the bracket. Doing so will straighten out any threads which may have been disturbed by the cutting and filing process. If you can't turn it out relatively easy by hand, then you should look for any rough edges or burs which might still be present. Repeat until all screws can be easily turned out, and you should be ready for mounting!