You can download the files without separating them into folders, follow these steps - 

1- Go to About Mass File Download tab.

2- Scroll down to File Download Configuration section and turn off the Download Zip of Files in Subfolders toggle.

3- Click on the Save button.


Refresh the other tabs if they are already opened, and then perform the download, you'll get your files without folder separation.


PS: View Mass File Download, Salesforce file download app on Salesforce AppExchange: https://appexchange.salesforce.com/appxListingDetail?listingId=a0N3A00000EcsAOUAZ