Open your audio editing software and load the original MP3 and instrumental tracks one below the other. The order is unimportant.
Line up the two tracks as closely as possible, using the visual peaks as guidelines. Playing both tracks at once can help you align them properly.
Select the instrumental track (depending on your program, this could mean simply clicking a button next to it or highlighting it) and look in the effects menu for the "Invert" option. Invert the instrumental track, then go back to display both tracks; notice how the peaks and valleys of the instrumental track are now directly opposite the corresponding peaks and valleys of the original MP3.
Zoom in as close as possible on either track to fine-tune the alignments. Make sure the files are exactly aligned; again, playing both tracks will help you determine if you need to make alterations and let you hear when the music has been canceled out to leave the a capella as clear as possible.
Save your file when you're satisfied with the a capella. In most programs, you can do this by selecting "File" and "Save As..." The resulting MP3 will be vocals only, leaving you with a custom a capella to use with your project.