Dear Spearing,
First and foremost, thank you for contacting National Instruments.
When you say that you want the user to be "isolated" from the shell VI, do you mean that you wish to set some security options that literally 'lock' the user out of the shell front panel and block diagram? If this is the case, you may want to look into the following:
Within the front panel of your VI, select [File]>>[VI Properties] and choose the [Security] tab under "Category".
Here, you can make the front panel password-protected, so that any given user can't modify the code during operation without supplying the correct authorization credentials.
Furthermore, you can select the [Window Appearance] tab under "Category" and select [Customize]. Here, you can cha
nge the options for the front panel to control whether the user can close the window, abort the shell VI, see the title and menu bars, etc...
I hope this helps you find a solution to your desired functionality. Please don't hesitate to ask for further support if needed. Have a great day!
Kind Regards,
Joe Des Rosier
National Instruments