Use a half inch mortising bit with a top bearing (see pix 1 below). Cut out a piece of 3/4 inch MDF exactly the width of the hinge (see pix 2 below). Use an oversized piece so you can rest the router on top of it so it won't wobble and mess up your mortise. Clamp several pieces of wood to the door so that the template you made rests securely on the edge of the door, supported by the extra wood. Set the depth of the router very carefully to the thickness of the hinge, then starting from the open area of the template, then into the wood.
Make sure you have the hinge on the correct side of the door before you start, and that the lock or latch is where it should be once hung.
If you are replacing existing doors and re-using the existing hinges, lay the old door against the new and transfer the hinge line from the old to the new door. That way, you only have to mortise the door, not the jambs.
If the jambs are new, you will have to place the hinges on both door and jamb. You can do this several ways, for example, mark the door first, then shim under the door so it fits precisely in the jamb, then transfer the marks to the jamb. Personally, I wouldn't cut the hinge mortises in the jamb with a router, I'd do it by hand with a chisel, somewhat like the following paragraph describes.
If your hinges are square, you will need to cut the rounded corners the router makes with a SHARP SHARP SHARP chisel. Did I mention to make sure it is really sharp? Use a little gentle hammer work to score the corner to the depth of the machine mortise. Then use the SUPER SHARP chisel to gradually cut out the wood in the corners.
If you're mortising the jamb, cut the outline with a sharp chisel and very carefully chisel out the mortise. Be careful not to take too much out. Get it as flat as possible. If you're replacing the jamb, consider locating the long screws that connect the jamb to the frame either under the hinge, or through a hole in the hinge.
It is harder to describe this than to do this process. Go slow, take your time, measure carefully. The second pix is of a simple shop made hinge mortising jig. The clamp is a must.