Thanks for your response
I used the same filter to not consider 0kb file for my actual payload process. The problem with that is, I ended up with so many suspended(resumable) messages and full of event logs saying there no port subscribed for these messages.
Finally, I had to create a send port subscribing to the 0kb files and routing them to a folder in the server.
Do we have an option in BizTalk with which we can simply delete messages matching with a particular subscription, without storing any where?