You'll just have to wait. If your website is crawlable and has a proper sitemap, Google will recrawl those pages, see that they're fixed and remove them from your Webmaster tools.
Yes, it's kinda annoying, but they're giving you a heads up to something you might otherwise not notice, which is pretty cool.
Just fix all the errors and they will disappear. I've had to do this for a website with a couple thousand errors (at launch). I just checked back every week to see what has changed. It can take a bit, but once they have figured out you are fixing it, the crawl rate will increase a bit and it will go (barely noticeable) faster :) You're not the only website with problems, you'll have to wait your turn.