Ok, I sold some of my rental houses this year ( actually all of them) and I got 1099 or a substitue 1099 for each of them,

I am looking at what I can apply agaist that sale, I have the amount of money I still owed on them, the real estate fee's, \

But I am wondering what I may also deduct, I spent many 1000's of dollars doing new floors, paint and a roof on one, would those exenses come off the top of the profits ? I also got the renters out prior to sale, to have time to fix them up, would loss of rents work toward it.

Just a general statement.

The taxable proceeds from the sale will be.
The selling price minus any cost of sale and the cost of repairs and improvements to the property in the recent past. There is a specific time but I don't know what it is.

That number minus you base, which is the original cost of the property minus depreciation is you taxable amount.
It is assume that you claimed any repairs, maintenance, depreciation and other expenses during the time it was rental property.
The money you did not receive when it was not rented is just that, money you did earn. It is not a loss and cannot be claimed as such.