No native way to apply filters using PAD actions. The best way to do it would be using scripting, such as PowerShell or VBscript. PAD supports both of these.
If you don't care about formatting, though, you can simply use Read from Excel worksheet instead of copying and pasting. When you read data, you end up with a data table variable. You can then loop through this table to find the rows that are relevant for you (essentially applying the filters in the flow, instead of the source file) and then use Write to Excel worksheet to write the values to the target file.
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