Good morning Restu,
This is the perfect forum for questions about Qiime 1.9.1. Welcome!
I'll focus on your final question:
These two files have been processed in different ways.
The filtered biom table (mc2) only has OTUs with a Minimum Count of 2. This will remove less common OTUs and is a very common filter.
In the rarefied table, each sample has been subsampled to an even depth, so that each sample has the same number of reads in it. This is a simple way to control for bias due to sampling depth (because it throws away the extra depth).
Does that help answer your question?
Now I have a question for you:
Is it OK to process your data slightly differently in order to do a valid statistical test and in order to make a clear graph?
My answer to this question is 'yes,' and I often use my rarefied data for a stat test, then merge replicates and filter OTUs so that my graph more simple. What do you think?