I'm a little confused on what it is you're trying to create.
Are your teams and structure already setup?
Are their rosters already filled or empty?
Do you need to add todays players and the previous years players as well or just the ones from previous years?
Are you trying to create an entirely new master.csv or just import players to your game?
I'm thinking you just want to add the players and the easiest way to do that is to open the master and do your sorting. Make sure all the players you want to keep have a bbref id in the bbrefid column (they should).
Delete all columns except the year and bbrefid columns.
Delete all rows you don't want. Save it as a .csv and rename the extension to .txt
Your txt file should look like this (bbrefid,year):
aardsda01,2009
aaronha01,1959
abreubo01,2000
adamsba01,1920
adamsmi02,2011
adamste01,2003
Copy the .txt file to your ootp stats folder or folder of your choice.
Now do a historical import and use the .txt file. That'll import all your players.
That's the easiest way to do it providing it's what you want to do.

If your version of excel can't handle all the rows in the master.csv your using, then get Apache Open Office. It's free, works perfectly, and will handle more than you'll ever need.