There are a couple of ways to approach this problem:
1- You could use the Run Script action and write a VBScript or JavaScript to remove the line from your CSV data file.
2- Or you could use the Data Mapper to filter out this record. How?
Set a Condition in your Data Mapper which checks whether your field has the targetted value. The field type can also be based on Automation properties. Check this guide for How to pass Workflow variables to the Data Mapper
Now in the True Branch (or False Branch depending on your condition), add an Action step and set the Action Type to Stop Processing Record