Removing A Stock Roof Rack

Morning guys. New to the group. I searched the forums but did not find an answer to my question. I haven't purchased my new project yet and that is part of my question. I am looking for a specific truck and I have found what I am looking for but it has the stock Toyota Tacoma roof rack runners on it. Has anyone removed these with success. I guess success would be with no leaks.
The Tacoma that I am looking for is the 4 door, 4WD with a 6 foot bed. Not the easiest to find and if I could purchase this one and remove the runners with no issues it would be great.
Thanks in advance

 

You can seal the holes but when I removed my oem rack the plastic pieces to hold the weather strip were broken and I had to glue the weather strip in. Not to mention it had damaged the paint on the roof and body above the doors

 

Im not as concern about the paint as I am a leak. Im going to repaint or vinyl wrap anyway. I have a full Yakima system I want to install and it won't work with that stock rack. If I can seal the holes successfully then it will work for me.

 

Just put flex shot in the holes