As far as I know MVC sample for EPiServer is for AlloyTech site (download here) which shows CMS capabilities.
If you want to setup MVC site using Visual Studio - this blog post may come handy.
When you are ready with MVC site then you can "apply" EPiServer Commerce stuff to it via Deployment Center. It could be done manually as well - but takes much more time :)
I am new to EPI server development. I want to create a single solution for a cms as well as ecommerce using visual studio 2012 (MVC based). But when i installed visual studio extensions for the episerver i could see only two templates to create a blank cms site. do we have any visual studio extension to create a blank ecomece site? how to create a custom ecommece site using visual studio ?? please help me on this issue.