How to capture execution plan from sql profiler for filtered queries only
The easiest way would be to stop using Profiler and go to Extended Events. The query_post_execution_showplan event has duration built right in and you can use that to filter capture quite neatly. Here's a simple example:
CREATE EVENT SESSION ExecPlansDuration
ON SERVER
    ADD EVENT sqlserver.query_post_execution_showplan
    (WHERE ([duration] &gt; (10000)))
    ADD TARGET package0.event_file
    (SET filename = N'ExecPlansDuration');

Just know that capturing plans can be very expensive.