I am new to using a 3d printer and I've been trying to learn about the build in the short space of time I have for this project. The 3d printer is a prusa i3 and uses an arduino mega. It has shields on it like a normal printer and I need to connect a rain sensor to the arduino in order to pause the printing process during rain. How will I connect the rain sensor to the Mega as I cannot get to the actual board because it is blocked with the shields and how will I add the code to the firmware files.
I think you would be more likely to get useful help on the RepRap forum which is all about 3D printing.
What program do you plan to use on the Mega? Unless you are writing your own code I suspect it may be difficult to arrange for an external input to pause the whole thing.
The mind boggles at the idea that printing must be stopped because of rain ? ? ?
Do you have the source of whatever software is currently installed on the Mega? If not, you're dead in the water with this project.
How to connect this sensor: well, that's another challenge as you'll have to find access somehow to one or more free input pins (either analog or digital, depending on your sensor). The shields are likely to expose all pins on top of them, as shields are normally stackable.
Forums that discuss your specific printer will be much more knowledgeable about those two issues for sure.