Check the WinMerge release notes:
Filters only applied when using full compare.
Line filtering is only applied in folder compare when using Full
Contents-compare method.
If you are using any other compare method, line filters are not
applied. Files marked different in folder compare can get status
changed to identical when opening them to file compare.
So, you will not be able to use regex to filter out the lines that are open in right/left pane.
You will have to install and use 3rd party filters, e.g. http://regexfilterforw.sourceforge.net/.