Native Pop Up Window from Unity window/linux build

Hi,
I am creating a non gaming software in unity. Since its a bit complex hence frame rate is low. I am rendering scene behind and in front, generating graphs and UI at runtime with the help of realtime data through DLLs.

I want to create window/Linux build exe, which should have buttons that on click can generate a pop up window which will turn would have another unity rendering , if i click some other button in exe it would pop up another window with certain different rendering/GUI etc.

I am not sure how to go about it i want to keep only one main unity build exe and get windows pop up having interactivity in them just like main exe.

Kindly guide me.