CMS generating thousands of links, will it hurt my SEO?

[clarybusinessmachines]

I've shifted my static (HTML) eCommerce website to Magento. I am facing serious problem, my website has total 20 products (each product has canonical URL) , I was surprised to see thousands of links indexed in Google as well as in my webmaster Crawler stats, later on I removed all from webmaster tool and marked as fixed, also blocked crawlers to crawl on those specific directories through robots.txt file.

Now my question is will these urls still effect my website's SEO? As they still exist and accessible but blocked for crawlers. And is there any better way to block them other than robots.txt.Thanks

[AlanMosley]

i would nott use robots.txt to block, as this means that the links now pointing to those pages are wasting their link juice. i would use a canonical on the pages to avoid duplicate content.

[IM_Learner]

I completely agree with Alan's views. Use of Canonical tags is most preferable.