Now before you begin designing your turtle pen, you need to do a bit a research on your specific turtle species.
Things to learn: (All examples are for Three-Toed Box Turtles)
-Male to female ratio, ex. 1:2
-Space needed for each turtle, ex. ~16 sq.ft
-Poisonous items, ex. cedar wood, sweet pea, ivy etc.(http://www.tortoise.org/general/poisonp.html
-Other odd facts that may be particular to your turtle
After you find out that information you should have a general idea of how big your turtle pen should be; now you can choose a location to build your pen. One thing to consider is amounts of shade and sunlight; you want your pen to get plenty of sun but still be shaded for a good part of the day, consider a spot near a tree. I would avoid placing your pen near your house or other building because when pest control comes(if they do) they spray poison around the perimeter of your house, and you don't want any of that to get near your pen. You should also consider access to a hose(something I didn't think of) to avoid having to pull a hose all the way across your yard.
Once you have decided on a location for your pen you can take some measurements, and begin designing the layout of your pen, and making a list of supplies(Make a trip to your local Home Depot or hardware store and take notes of what they have before doing this). You can go ahead and buy everything now or buy it throughout the process.