RCCE is still designed to work on baremetal, but work on its baremetal version is not as up-to-date as work on its SCC Linux version. So in the near future you may come across issues when working on baremetal.
MS_BAREMETAL refers to Microsoft's baremetal Visual Studio plugin. This plugin is not currently publicly available.
By modifying page tables, you are essentially modifying the OS. I don't think this is something you would want to do (even if you could) from the application level. The source code for SCC Linux is available, so you can investigate that area if you want.
So, you mean at this moment, I cannot use baremetal version, right?
Could you estimate how long I need to wait to use it? 3 month? or 1 year? 
We'll have better baremetal tools for you in weeks, not months, but you can use baremetal now. However, you are currently on your own.
MIcrosoft released a baremetal plugin for VIsual Studio today. I think over the next few weeks we should gain some experience using it which we can share with you.
http://research.microsoft.com/en-us/downloads/37ccb116-c67d-4c44-9181-898889b8352d/
There is at least one other group doing baremetal work successfully, but I don't know how close they are to going public.
The intent here is to share as much as we are able to on how researchers are using the SCC in a baremetal environment.
