Friday, the state police searched the organization's building on North Main Street.
According to search warrants filed in Grayson County Circuit Court, police removed 30 boxes of documents, computers, hard-drives and file folders.
The program director Christian Bedsaul and assistant Sharon Nichols are named on the search warrants and are under investigation for misusing federal, state and local dollars while working for Rooftops of Virginia.
Rooftop of Virginia money was used for personal loans to employees as "salary advancements" and for personal airfare travel, according to the warrants.
Police are looking at the non-profit's financial data dating back to 2006.