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As per subject, I got this error message using Metaio SDK in Unity5. BTW, I'm using Mac, not Windows machine.

Plugin 'MFC100U.DLL' is used from several locations:
 Assets/Plugins/x86_64/MFC100U.DLL would be copied to <PluginPath>/MFC100U.DLL
 Assets/Plugins/x86/MFC100U.DLL would be copied to <PluginPath>/MFC100U.DLL
Plugin 'MSVCP100.DLL' is used from several locations:
 Assets/Plugins/x86/MSVCP100.DLL would be copied to <PluginPath>/MSVCP100.DLL
 Assets/Plugins/x86_64/MSVCP100.DLL would be copied to <PluginPath>/MSVCP100.DLL
Plugin 'pthreadVC2.dll' is used from several locations:
 Assets/Plugins/x86/pthreadVC2.dll would be copied to <PluginPath>/pthreadVC2.dll
 Assets/Plugins/x86_64/pthreadVC2.dll would be copied to <PluginPath>/pthreadVC2.dll
Plugin 'Shore140.dll' is used from several locations:
 Assets/Plugins/x86_64/Shore140.dll would be copied to <PluginPath>/Shore140.dll
 Assets/Plugins/x86/Shore140.dll would be copied to <PluginPath>/Shore140.dll
Plugin 'MSVCR100.DLL' is used from several locations:
 Assets/Plugins/x86/MSVCR100.DLL would be copied to <PluginPath>/MSVCR100.DLL
 Assets/Plugins/x86_64/MSVCR100.DLL would be copied to <PluginPath>/MSVCR100.DLL
Plugin 'metaiosdk.dll' is used from several locations:
 Assets/Plugins/x86/metaiosdk.dll would be copied to <PluginPath>/metaiosdk.dll
 Assets/Plugins/x86_64/metaiosdk.dll would be copied to <PluginPath>/metaiosdk.dll
Please fix plugin settings and try again.

UnityEditor.Modules.DefaultPluginImporterExtension:CheckFileCollisions(String)
UnityEditorInternal.PluginsHelper:CheckFileCollisions(BuildTarget) (at /Users/builduser/buildslave/unity/build/Editor/Mono/Plugins/PluginsHelper.cs:25)
UnityEditor.BuildPlayerWindow:BuildPlayerAndRun()

How I can fix this error? Please advice. Thank you.

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You have multiple versions of the dll that are both set to be used for the same platform or cpu. Unity 5 introduced new plugin settings so that you can compile different versions of the same dll, but you need to specify which platform or cpu each version is for. Checkout this link for more info.

http://docs.unity3d.com/Manual/PluginInspector.html

(Note: I originally gave this answer on Unity Answers. http://answers.unity3d.com/questions/988343/plesehelp-meplugin-systemdatadll-is-used-from-seve.html#answer-1017015)

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