everyone thinks vertical, try horizontal
Using a portable electric drill lay it flat on the bench with a long drill or rod in the chuck. See what thickness block it would take under it to make the rod parallel with the bench top, then tape it on the body of the drill. Now you always have a hole that is parallel to the bench top.
Next lay your work on the bench top and space it so that the hole is where you want it. Then drill your hole making certain to keep the work parallel with the drill or the edge of the bench. One axis will be true, the other axis you'll have to eyeball.
Another approach is to make a jig with an angle block that rides the sides of the work and is parallel to them. Tape your drill on the inside of the angle block so the drill is where you want it.... in the center. Now slide the jig along the work so it drills the hole parallel to both sides.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)