Of course you can!
You just need to keep in mind that designing your controller is just to come up with one or several equations. Let say you are going to design a proportional controller for your system: in its simplest form, at the end you just need to find out a constant number.
Make sure you understand which parts of your system that are going to be done by the computer. The best way to do that is to draw your block diagram, breaking each block as much as possible depending on the necesary parts: the knob to set the temperature, the D/A and D/A converters, etc. You should be able to draw a circle enclosing the computer side from the external side. Once you do that and understand how is your system, the rest is almost mechanical...
... until you get t
o the implementation. Keep in mind that the real thing will behave sligthly different than your mathematical models, and you need to "tweak" your system a little to obtain the best performance. For example, maybe you are heating a rod or something that you assumed for simplicity that is perfectly homogenous. Chances are it is not and the temperature gradient and distribution will not exactly follow your model.
This is a high-level answer and I am pretty you will get more answers and commentaries. Now, about how to do it...
Regards;
Enrique
www.vartortech.com