Disclaimer: In this example I modified CodeAssassin.ConfigTransform.targets directly. But you should create a separate .targets file and reference that in your .csproj.
Add a ConnectionString.config (as an example) and then add the transforms.

Add this to the .targets file (your config name just has to match the regex expression - (?i)^ConnectionString\.
in this case):
<Target Name="TransformAllConnectionStringConfigTransformFiles"
Condition="'$(WebProjectOutputDir)'!=''"
BeforeTargets="Compile">
<ItemGroup>
<ConnectionStringConfigTransformFile Include="@(None);@(Content)" Condition="'$([System.Text.RegularExpressions.Regex]::IsMatch(%(Filename),"(?i)^ConnectionString\."))' == true and '%(Extension)'=='.config'" />
</ItemGroup>
<TransformXml Source="ConnectionString.config" Destination="%(ConnectionStringConfigTransformFile.Identity).transformed" Transform="@(ConnectionStringConfigTransformFile)"
Condition="'@(ConnectionStringConfigTransformFile)'!=''" />
<CreateItem Include="%(ConnectionStringConfigTransformFile.Identity).transformed"
AdditionalMetadata="CopyToOutputDirectory=Always">
<Output TaskParameter="Include" ItemName="Content"/>
</CreateItem>
</Target>
Build, and your .transformed files are created.
