How to find files over certain limit in SharePoint Library with hundreds of folders

HI luvsql 

Great that it is working

The following line is that one that will need to change

#Get All Files of the library with size > 100MB
$Files = Get-PnPListItem -List $List -PageSize 500 | Where {($_.FieldValues.FileLeafRef -like "*.*") -and ($_.FieldValues.SMTotalFileStreamSize/1MB -gt 100)}

The # means comment out this line i.e. it tells the programming language to ignore this row

So I suggest you change the script so it looks like this , removing the part after the -and  statement

#Get All Files of the library with size > 100MB
#$Files = Get-PnPListItem -List $List -PageSize 500 | Where {($_.FieldValues.FileLeafRef -like "*.*") -and ($_.FieldValues.SMTotalFileStreamSize/1MB -gt 100)}

#Get all files, of any size
$Files = Get-PnPListItem -List $List -PageSize 500 | Where {($_.FieldValues.FileLeafRef -like "*.*") 

I can't see anything in the script which will limit it to just 2 folders deep.

It may be that there are NO files larger than 100MB that exists in folders lower than 2 folders deep.

Microsoft have some training about PowerShell

https://docs.microsoft.com/en-us/powershell/sharepoint/sharepoint-online/connect-sharepoint-online?view=sharepoint-ps

as do a number of prominent SharePoint online authorities

https://www.google.co.nz/search?q=how+to+learn+powershell+for+sharepoint 

Everyone who does our kind of work, can get value out of knowing something about PowerShell, so I highly recommend learning a little about it. I prefer dealing with people and the social anthropology side of my job, but there are times when Powershell makes things possible that wouldn't be otherwise.