Compare All Rows In One Table Against Another Table?

I've got a table in an SQL server that often has large amounts of data imported into it via an automated process - the problem is that a lot of the data that gets imported is a duplicate of data that is already in there (for example if we have a customer in there called Mr Customer Ltd, a duplicate with a slightly different name could get imported, like Mr.Customer Ltd).

So I am using the Fuzzy Logic class that Wild Bill put in the CodeBank to find names that are similar and then highlight these items. The thing is that the target table that the imported data ends up in has several thousand rows and the table that contains the data to be imported often contains several thousand rows as well, so I'm trying to decide how to do this. Obviously reading both tables into memory is not an option as it will consume too much memory on the client PC that is running this app. So this is what I am doing at the moment:

1. Read the table that contains data to be imported into a DataTable in memory

2. Open a connection to the target table and use the SQLDataReader to start to loop through it

3. In this loop, for each row that the data reader reads I then loop through the entire set of rows in the DataTable and run this fuzzy logic method that compares the account name from the current row in the datatable loop to the account name in the row that the datareader is currently on.(there is also a Thread.Sleep(1) after each row is processed to prevent the process from eating up 100% of the CPU while it runs)