To get the files copied to the Publish Target Location, please make the following changes:
1) In your References, please set "Copy Local" property of PDFNet.dll to "True"
2) Add the following to PublishProfile i.e. *.pubxml
<Target Name="PDFNetFiles">
<ItemGroup>
<_CustomFiles Include="bin\**\*" />
<FilesForPackagingFromProject Include="%(_CustomFiles.Identity)">
<DestinationRelativePath>bin\%(RecursiveDir)%(Filename)%(Extension)</DestinationRelativePath>
</FilesForPackagingFromProject>
</ItemGroup>
</Target>
Under PropertyGroup:
<CopyAllFilesToSingleFolderForPackageDependsOn>
PDFNetFiles;
$(CopyAllFilesToSingleFolderForPackageDependsOn);
</CopyAllFilesToSingleFolderForPackageDependsOn>
<CopyAllFilesToSingleFolderForMsdeployDependsOn>
PDFNetFiles;
$(CopyAllFilesToSingleFolderForMsdeployDependsOn);
</CopyAllFilesToSingleFolderForMsdeployDependsOn>
ASP .NET Deploying extra files: