While reading the document library you can exclude the system related document library. Below are the list of system libraries in SharePoint, you can exclude the below list/library.

$systemlibs =@("Converted Forms", "Customized Reports", "Documents", "Form Templates", "Images", "List Template Gallery", "Master Page Gallery", "Pages", "Reporting Templates", "Site Assets", "Site Collection Documents", "Site Collection Images", "Site Pages", "Solution Gallery", "Style Library", "Theme Gallery", "Web Part Gallery", "wfpub") 

Refer to the below example:

Powershell - get a list of all the document libraries for a web application including content types - output to csv

How exclude the system related files while reading the document library in SharePoint?

You can refer to the below example to exclude system related documents, this example is in c# coding, however you can get the equivalent PowerShell object.

How to exclude hidden/system sharepoint files when enumerating a document library

While reading the document library you can exclude the system-related document library. Below is the list of system libraries in SharePoint, you can exclude the below list/library.

$systemlibs =@("Converted Forms", "Customized Reports", "Documents", "Form Templates", "Images", "List Template Gallery", "Master Page Gallery", "Pages", "Reporting Templates", "Site Assets", "Site Collection Documents", "Site Collection Images", "Site Pages", "Solution Gallery", "Style Library", "Theme Gallery", "Web Part Gallery", "wfpub") 

Refer to the below example:

Powershell - get a list of all the document libraries for a web application including content types - output to csv

How exclude the system related files while reading the document library in SharePoint?

You can refer to the below example to exclude system related documents, this example is in c# coding, however you can get the equivalent PowerShell object.

How to exclude hidden/system sharepoint files when enumerating a document library