There is a bug in the binaries from Nuget as well as zip files uploaded on apache site for Lucene.net. Chained filter class is not available in the Lucene 3.0.3 build (binaries) even if you download it from NuGet.
I downloaded the source and noticed that the ChainedFilter.cs class is present in the Apache-Lucene.Net-3.0.3-RC2.src\src\contrib\Analyzers\Filters folder, but this folder is surprisingly not a part of the Contrib.Analyzers project. That is why it was missing from the generated binaries.
I added it back again, but then got a compilation error on the MaxDoc() property being used a method instead of a property. I changed MaxDoc() to MaxDoc and the build worked and used the generated binaries in my own project without any issues.