I’m interested in applying as a transfer student to a few colleges where I was rejected as a freshman applicant. Will they be able to pull up my previous application in their system? Or do I get a fresh start?
Yes, most colleges will keep your application on file for at least a few years. That’s why they ask if you’ve applied previously on transfer applications. If you answer yes to this question, colleges will pull up your old freshman application, including your high school transcript, and compare it to your transfer application. For this reason, you should avoid duplicating anything you wrote on your original application (i.e. don't use the same essay over again). You should also be sure to strongly emphasize how you've grown since your original application. What academic and personal strides have you made in the past year or two that make you into a better candidate than you were as a high schooler?
Many colleges will keep your application indefinitely, or at least the fact that you applied and were rejected. Harvard University is known to keep every application indefinitely, and it shares applications between the different divisions of the university. It uses this policy to enforce its rule on the maximum number of times you can apply to Harvard's grad schools in a lifetime (three).