If there are certain files or folders you don't want to include in your sitemap, you can easily tell Sitemapper to ignore them while it's scanning your website. Just click the Settings button in the Toolbar and you'll see the URLs and Queries to Ignore fields. Let's say you want to ignore a certain file. Just click the Add button next to the Files to Ignore field and enter the URL of the file you want to ignore in the given field. When you're done, click OK. The file will automatically be added to the ignore list. The process is the same for folders. Keep in mind that when you ignore a folder, you're also ignoring all the files it contains.
When you're done configuring your ignore lists, you're free to scan your website. None of the files or folders you specified will appear in your map.