Well I could not get "Intersect Faces>With Selection" to work, which isn't surprising it has taken me two or three days to get most things to work.
But I did have a relatively easy answer.
I removed/deleted the hexagon and the hole then redrew the hexagon and pushed it to it's depth and then redid the circles drawn on the hexagon face and pushed the circle to the bottom.
Now a funny thing was from the Top view I could see through the bolt holes to my background but when viewed from the bottom there were no circles/holes!
So I drew the circles on the bottom and pushed the holes through.
Well there ya go, learning more every day. My 3D printer "should" ship around the end of March so hopefully I'll have some good models to print by then.
Thanks for the great help,
Ralph