A couple more tips:
Lay some sandpaper on a flat surface and rub the bottom of the saddle on it the long way. Use rough sandpaper (around 120 grit) to remove the bulk and smooth it out on fine sandpaper (around 400 grit). Three things to worry about are:
1.) Keep the saddle perpendicular to the flat surface - don't let it lean over while sanding. I lay a square steel block on the sandpaper and run the saddle along it to keep it square.
2.) Scribe a line before sanding so you don't take uneven amounts off of the bass or treble side. Sand slowly up to the line, checking it frequently to make sure it's even.
3.) Use even pressure across the whole saddle while sanding. A saddle is flexible enough that if you only push down in the middle, then more material will come off of the middle and leave the bottom curved.
Of course, sometimes a curved bottom is desirable. If your guitar's top has a belly then the saddle slot in the bridge will have developed a curve as well. It's very tough to determine without special tools but matching the saddle bottom curve exactly with the saddle slot bottom is ideal, especially if there's an undersaddle transducer (pickup).