Have you tried clicking the edge of a hole and hitting the delete button? There is a hidden feature called "Delete Hole" that I use all the time for what you are doing there.
Mohamed, can you upload your part for us to look at? Thanks.
Are you wanting to fill that entire area with holes? If so, use the fill pattern command. You may have to play with it to get the desired result....
I think untrim will do what you want