Not entirely, except if you remove or disguise all Magento features. But you can make it harder:

- change admin URL, remove downloader directory (you should do that anyway to protect your store)
- show "404 Not Found" status for forbidden directories like `shell` and `var` instead of "403 Forbidden" to not give away their presence. See http://magento.stackexchange.com/questions/16504/recommended-method-to-protect-downloader/98322#98322
- change base directories for skin and media, because the typical image paths are easy to recognize
- Don't build your theme skin upon any of the default base themes and remove those from `skin/frontend`, otherwise it is possible to recognize the default style sheets (see: http://magento.stackexchange.com/questions/60476/determine-magento-version-without-access-to-code-base/62966#62966)
- Change the URL routes for pages like customer login, checkout or product reviews. There are extensions that help you with that, like https://github.com/klein0r/magento-language-routes

Doing all this just to disguise that you run on Magento is quite expensive, if you did not already build a theme from scratch with no default templates and styles, so you have to decide if it's really worth it.