<?xml version="1.0" encoding="utf-8" ?>
<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
    <Target Name="ILRepacker" AfterTargets="Build" Condition="'$(Configuration)' == 'Release'">

    <ItemGroup>
	<InputAssemblies Include="$(OutputPath)$(TargetName)$(TargetExt)" />
        <InputAssemblies Include="$(OutputPath)MyAnotherDll.dll" />
    </ItemGroup>

    <ILRepack
	  Parallel="true"
      DebugInfo="true"
      AllowDuplicateResources="false"
      InputAssemblies="@(InputAssemblies)"
      TargetKind="SameAsPrimaryAssembly"
      KeyFile="$(KeyFile)"
      OutputFile="$(OutputPath)merged\$(TargetName)$(TargetExt)"
    />

    </Target>
</Project>

The process cannot access the file 'bin\Debug\MyAssembly.pdb' because it is being used by another process.