As I recall, yes – the FAFSA asks for the net worth of investments, so that would be the value minus what is owed. The CSS Profile will ask for more detail than that but will take into account what is owed on the value of the assets.
But, if your parents are receiving rents from the properties, that will count as income and if it is high enough it may preclude you from need-based aid.
Tagging @BelknapPoint and @kelsmom for further comments and to correct me if I am wrong.