Instead of giving “back to top” button is it good to make layout with fixed header and footer for better usability? or this type of layout can be problem for screen reader?
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This would be determined on a case-by-case basis. Some pages have minimal headers with crucial information, while others have bloated headers with useless information. As for screen readers, as long as your structure is consistent (and you do the sticky with css/javascript) I don’t think there would be any problem.
Just keep in mind that stickied items take up screen space. With many people browsing the web on laptops and mobile devices, that screen space may be more crucial than you think. Don’t sticky a header and/or footer unless it’s absolutely necessary.
Perhaps an alternative method would be helpful. Maybe instead of your links saying “Back to top,” they simply said “Popup Navigation.” When clicked, a small div appears with the navigation (since this is what users typically go back to the top for). I worked up a quick example: http://jsbin.com/uromo/2/edit