I have been paying my father $500 a month for the past year for a personal loan I owe him.I will be filing bankruptcy in the next few months. If the trustee see's this activity on past bank accounts, will he come after my dad?How can this be avoided?

What you are describing is a 'preferential transfer' or 'preference'. The bankruptcy forms have a question about who you have paid and how much, during the previous two years, I believe. Try not put yourself in a position where you fail to disclose the truth.
Chapter 7 Trustee's Powers-What is a Preference? : Bankruptcy Law Network (http://www.bankruptcylawnetwork.com/2007/08/12/chapter-7-trustees-powers-what-is-a-preference/)