how to close these holes?

 From:  BurrMan
5480.6 In reply to 5480.4 
Select one of the top edges and copy and paste it.

Go to the right view and grab one of the edit frame handles and "sqeeze" the surve until it says "flat"

Move the curve to the front a bit.

Run seperate on the surface object and delete the bottom planar surface.

Do an Edge selection on the surface and hit Ctrl+A to select all edges and hit delete.

Select the hollow cylinder and run Construct-Planar

Use boolean diff on the cylinder with the extracted edge.