Okay so my friend is going on Facebook and telling my girlfriend Lies, Like I cheat, Flirt with other girls etc. I logged onto her Facebook and deleted the messages because I'm scared that she'll believe him and not me?
I'm not sure logging onto her Facebook without her permission was a great idea, if she finds out - it will only make you look guiltier and reinforce the idea that you are untrustworthy.
I would suggest sitting down with her and talking about this guy, and his possible motives for trying to sabotage your relationship. Does he like her too?
Tell her you want to protect her from being hurt by this jerk and ask her advice on how to handle the situation, she will probably appreciate that you confided in her and sought her advice... Trying to sort the situation out by going behind her back is a risky strategy.