A command similar to the following should work
msbuild YourSolution.sln /tv:3.5 /p:TargetFrameworkVersion=v3.5
or
msbuild YourSolution.sln /p:TargetFrameworkVersion=v3.5
/tv (or /toolsversion) Indicates which version of the MSBuild tools you want to use, and the property TargetFrameworkVersion indicates the target framework. In your case just specifying that property should be fine, but if you want to use the 3.5 MSBuild toolset you can sepcify it with /tv as I did in the first command.
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