I've had this problem since I moved up to 10.6

I validate fonts w/Font Book. I get the list of fonts with errors. But when I click Remove, they're not removed. If I validate again, the duplicates still exist.

In the past, I went through folders where I found fonts, then moved them to a separate folder in my Documents folder, but I don't want to do that again, considering I didn't really know what I was doing. I don't want the system to add fonts wherever it finds them.

I wondered if there is a program or a method to make this job easier.

I remember when font handling was something Apple was proud of. It's more complicated than OS 9.

Recently I re-installed 10.6.3 and I'm not sure what to do.

Since I am running Mavericks (OS X 10.9) FontBook 5.0.1 may work a bit differently than your version, but I don't think Font Book has changed much over the last several years. In 5.0.1 the font to be deleted is selected by placing a checkmark in the check box to the left of the font name and then click on "Remove Checked" at the bottom of the Font Book window. At that point a verification dialogue should appear near the top of the window reading "Are you sure you want to delete checked fonts" and at the bottom right of that dialog are two buttons one labeled Cancel and the other labeled delete. Clicking the delete button should immediately remove the font.