How do you remove permanent marker stains from carpet? Well, the bad news is that it's called "permanent" marker for a reason. Depending on how new and how deep the stains are, you may not be able to remove them completely.You can almost always lighten stains, though, and sometimes make them unnoticible. There are other things you can do to hide the stain as well. Start with the method here to get out as much as you can.First, thoroughly vacuum the area. This removes any loose dirt, dust or othe.