I had to remove my project from eclipse entirely. To do so I copied the folder of my project in workspace and pasted it onto my desktop. Then navigated back into eclipse right clicked selected delete and then check the box to delete the project from my workspace.
After this I closed eclipse. Opened Android studio and tried to open my imported project. At this point it told me the project didn't exist and provided me with an option to remove it from the list. After clicking this i closed Android Studio, and when i reopened it the project was gone.
Finally, I reopened eclipse and imported my project from existing sources to get it back inside eclipse.
NOTE
I would advise against using Android Studio on projects that you have that already work fine with eclipse. Android studio is cool when you are creating new projects but from my experience there are a lot of problems with build paths when I import a build.gradle from eclipse to Android Studio. Android Studio is great but remember it is still in the I/O pre-release!!!
--Just my 2 cents!