Handle duplicate removals in huge excel files

So we have huge excel files in various formats that we sometimes must double check against each other and remove duplicates from file A that exists in file B. In short we put all the info that will be matched in column A in both files. Then we use to run a MACRO but it takes hours for huge files so we need a better solution. Maybe access or similar? The files can have different amount of columns from time to time but column A will ALWAYS have the info that will be matched. So File A) is matched against file B) and the output file will be file A) with all the UNIQUE rows intacs. In other words all the rows that file B) has that matches with file A) are removed from file A) And the rest is output. I need this done ASAP since we have a file of 1,5 million rows that we need to match agains a file with about 200k rows and I can't use a macro for that since it's too slow.