With Eye P.A. and Wireshark, you can use Eye P.A. to filter or drilldown on packets, and then use Wireshark to save only the filtered to a new PCAP file.
Save Filtered Packets with Eye P.A. and Wireshark
1. In Eye P.A., apply the desired filters using the Filter Bar, or drilldown into the desired conversation with the multilayered pie charts.
2. Click File > Send to Wireshark
3. In Wireshark, click Edit > Mark All Displayed Packets.
4. Click Edit > Export Specified Packets...
5. In the Export Specified Packets window, name the PCAP file and Save it with the default settings.
6. You will have now saved a PCAP file that only contains the frames that you selected or filtered in Eye P.A.