For those interested in the solution here is how to do it:
Open you project in Atmel Studio 6 Go to the solution explorer and right click on the project. Select "Unload project" Now the project should be colored in gray. Right click again on the project and select Edit.
You will see the xml code from the configuration and settings of the project.
Around line 50 more o less you will find these lines:
<Language>C</Language>
<ToolchainName>com.Atmel.AVRGCC32.C</ToolchainName>
And modify them as follow, changing the language:
<Language>CPP</Language>
<ToolchainName>com.Atmel.AVRGCC32.CPP</ToolchainName>
Right click on the project again and select reload project.
Now if you go to the properties of the project (CTRL + F7) you will see two compilers in the Toolchain. Now you can compile both C and C++ code.