extract only payload parts of packets of pcap file

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It's not clear what you want to do. It's not possible to put the payload of say UDP and put it in a readable pcap file as it would require a pcap link type of the protocol running on top of UDP for a program to be able to read that file. ( Link to pcap file format However there is the "Exported PDU" functionality that can export some payload data and put it in a new file together with meta data which makes it possible to read the created file. It does not work for all possible payloads though.