There are three basic approaches:
1. make or purchase a mortising jig that is oriented to using a plunge router with guide bushings for most of the work, and then clean the corners with a chisel (or, round the corners of the tenon to fit),
2. use a mortising machine or drill-press attachment (these typically cut relatively small, standard sized mortises (3/8", 1/2", 5/8", etc.) in stock of any width), or
3. mark the piece and cut them by hand with mortise and regular bench chisels.
Methods #1 and #2 are pretty straightforward, with the accuracy of the machine technique providing the confidence level. Method #3 requires more skill to keep the cheeks of the mortise square, and the confidence results from practice.