Can we create three level folder structure in SDL Media Manager? As per documentation we can create only two level folder structure, but my requirement is to create three level folder structure to categorize assets furthermore.
No, currently Media Manager only supports Folders and Subfolders, as you've already seen in the documentation.
For customers that have needed additional granularity I have used multiple Clients, which can act somewhat like Folders at the level above them. You can also use multiple Accounts for another level, though you must be careful with Tags, as they are Account specific.