Permalink not working in my theme

I’m using wordpress 3.5.1 version.

I developed a new theme by following the below steps,

a. copied the existing twenty twelve theme and renamed the that theme as my new theme
b. modified the twenty twelve theme name in the style.css file with my theme
c. later, modified my theme for the client requirements.

Everything works fine until I change the permalinks from default to postname. All my pages are treated as 404 page.

So please support me to fix this issue.

Regards,
Sri