The first thing I do is see if what I want already exists. If it does, I buy it and smile broadly. That failing, I break out my swiss files and start in. I usually flatten the head and polish it on my polishing wheel before anything. Next I shape the outline shape and bevel the head if the stamp will need that (this is for bevels or other such stamps). With the general shape done, I make large cuts with a medium-sized fine flat file and detail work with swiss files. I've made raised dots in the stamps with a center punch and shaped the tool around those impressions.
Here is a pic of three stamps I've made. I chose these three to show it doesn't matter how nice the bolt is to make a good stamp. Once you file through the rust or finish, the steel is the same. The other photo is a close-up of the smaller flower one. You can see how I made an impression in the center with a rounded center punch, next shaped the outside and finally finished it with swiss files.