What do you mean by invisible?
Any system changes should be done in deferred execution.

System changes such as installing files should always be performed in the deferred sequence, as this is where functions such as rollback are active (in case of an installation error).
No files in an MSI are invisible. This is an open installation format and any competent MSI packager can easily extract the content of any MSI.

Perhaps, as AngelD has requested, a clearer explanation of what you mean by "Invisible" will enable us to better answer your questions.

If it is something as simple as setting the file attributes to "system" so that the standard user cannot see them by default, then that's easy to implement, but before we launch into explanations, it would be better if we were to be sure what you are asking.