Not with any guarantee of reliability anyway.
You can use a robots text file to encourage indexing of your pages or even to disallow indexing of some of them, but the trouble with frames is and always has been that one page is typically made of two or three different html documents displayed at the same time, so a search engine simply reads the main page and indexes it. It doesn't give two hoots whether your navigation links are on a left, top or bottom panel. It is only concerned with the main page content.
Frames look good when done properly, but the majority of web designers give them a very wide berth for this and other reasons. You can achieve more or less the same results by and large with clever use of tables on a single page and you have the advantage of full search engine indexing.
Sorry to be the bringer of bad news, but there you have it.