Eagle Ground Pour Fills Drill Hole
I don't know how you transfer your EAGLE layout to whatever you use to etch your board.

If you simply print the layout, make all layers except TOP, PADS and VIAS invisible, because all visible layers will be printed. In the printer menu, choose

[x] black
[ ] filled

The unchecked "filled" options makes holes appear as such, and not covered by copper:



I prefer a CAM job, since it allows to select the layers separately and can generate files for top and bottom in one go. There, the option is  called "fill pads" or similar.

(I don't have the english version here, so the options might be called slightly different)