Software Deployment

Sorry, but I'm not sure I understand your question.

If you mean that you have an EXE which extracts and runs several MSI, then no, do NOT re-capture. Make any customisations you need via a transform, using Wise's InstallTailor tool, for each.

We need one main MSI atleast onwhich we should apply MST , how should we proceed in this case where we dont have one MSI , instead exe.

OK, so let me guess again...

You have an EXE which does some installation tasks but it also extracts and executes some MSIs?

In that case:
- run the EXE on your packaging box. When the various MSIs appear in your %TEMP% folder, copy them somewhere, then rename them using easy-to-remember names.
- restore your packaging box to its state before you ran the EXE
- run the various MSIs
- NOW capture the EXE.

This way, your capture won't include the running of these MSIs, because Windows Installer will see their installed state and therefore do nothing.