Can I have the scanner only scan certain parts of my website?

Yes, you can. Go to the Scans tab and under Crawler Settings in the "Included URL Prefixes" textbox you can set the relative URL prefixes to determine which parts of your website you want the scanner to crawl. For example /en would only crawl pages on your website that start with the URL /en. Leaving this field blank will scan all URLs on your website.