There are a couple of reasons why you might want to 'lower' the saddle slot in your acoustic guitar's bridge. Most of the time, this is necessary when you're installing an under-saddle pickup. These pickups are usually a strip of piezo-electric crystal that sits in the bridge slot, under the saddle (hence the name).
Of course, popping in a pickup that's a couple of millimetres thick means that your saddle then sits higher in the slot, raising the action and possibly making for an unstable saddle.
The answer, in most cases, is to rout the slot a lower. This makes room for the pickup while meaning the saddle sits, comfortably at its original height.
The routing is done with a Dremel-style tool, mounted in a router base. The important part of this work, however, is taken care of by that slightly complicated looking acrylic jig. Guitar guys used to have to make their own jigs for this but you can buy one now. That's a much easier way to go.
The jig adjusts so that your router run matches the angle of the saddle slot and it includes a 'stop' at either end so you don't accidentally make your slot longer. It's a bit fiddly to set up but, once it is, the job is made much easier. Hurrah for clever jigs.