My site has 46 Error pages (404 error- page not found) from webmaster account. Its can effect on my site traffic and keywords ranking? And how can i remove these pages from search engine? Please suggest..

If coming from internal links:
Fix them

If coming from external backlinks
Just 301 (permanent redirect) them to appropriate/most-relevant pages

You can simply intimate the Google through webmaster tool.

In Google Webmaster tool there is a option to remove the error URL them from Crawling.
Click On
Site Configuration --Click--> Crawler Access --Click--> Remove URL

hi
this error comes due to broken link check  for broken links.

HI.
Yes it can harm your ranking on the search engine. You can remove thses errors with the 404 custom page & redirect all these errors into this page.

HI.
  Surely, it will effect your page ranking. if you are getting error 403 then delete these errors by using 404 custom page. In this way all these errors will redirect to this page.

If you found 404 error within your site then check the broken link and resolve it. If not means it comes from other sites then you go on that sites and if possible send the request to webmaster of that sites to change the url, or if there is edit option then you can do it yourself.

HI
yes surely this going to effect, so its better to remove , you can use 302 redirect to redirect the traffic.