##Disclaimer##
I'm generally new to electronics, so if my questions come across as stupid please bare with me. We all have to start somewhere.
##End##
OK. I will give you a brief outline of my project. I am attempting to run Snort on my Arduino. I am doing this using a microSD to store and run the program from.
Th problem I am having is that, I don't know how to run a program from the microSD. If someone give me some guidance/tips on how to achieve this, it would be greatly appreciated.
I don't know how to run a program from the microSD
you can't. Best you can do is to have an interpreter running that reads commands from the sdCard.
What is snort?
I am attempting to run Snort on my Arduino.
Not gonna happen.
The arduino has no operating system, few resources, and is the wrong architecture for a typical linux application.
-j
What is snort?
I have to ask the same question, because I'm at work, and afraid to Google it... 
google => Snort® is an open source network intrusion prevention and detection system (IDS/IPS) developed by Sourcefire.
RIGHT, that is a bit disappointing. What would I need to get this project going, an embedded Linux system of some kind?
If you've got a bit of time on your hands
probably the new Raspberry PI would be able to run it ... - http://www.raspberrypi.org/ - so new you almost cannot get one yet ...
I am doing this using a microSD to store and run the program from.
Try PyxisOS for Arduino that can run programmes from SD card.
You need , A Mega, A color touch LCD , SD card shield.