It'll be better to store folder structure in a single table, rather creating a table for each folder. 
For example, such table could have structure like:
╔═══════════╦══════╦══════════════════════════════════╗
║  Column   ║ Type ║           Description            ║
╠═══════════╬══════╬══════════════════════════════════╣
║ id        ║ int  ║ Unique identifier of the folder  ║
║ parent_id ║ int  ║ id of the parent folder          ║
║ name      ║ text ║ Name of the folder               ║
║ mpath     ║ text ║ Materialized path of parent id's ║
╚═══════════╩══════╩══════════════════════════════════╝
Note about materialized path: it is optional, and could be added to make it faster to run queries like "Get all children of folder 123" without recusive calls.
So, let's pretend you have this folder structure:
/
├── home/
│   ├── aspiring-master
│   │    └── .bashrc
│   └── guest-user
└── var/
    ├── log/
    └── lib/
It could be presented in form of mentioned table like this:
╔════╦═══════════╦═══════════════════╦═══════════╗
║ id ║ parent_id ║       name        ║   mpath   ║
╠════╬═══════════╬═══════════════════╬═══════════╣
║  1 ║ null      ║ "/"               ║ "/"       ║
║  2 ║ 1         ║ "home"            ║ "/1/"     ║
║  3 ║ 2         ║ "aspiring-master" ║ "/1/2/"   ║
║  4 ║ 3         ║ ".bashrc"         ║ "/1/2/3/" ║
║  5 ║ 2         ║ "guest-user"      ║ "/1/2/"   ║
║  6 ║ 1         ║ "var"             ║ "/1/"     ║
║  7 ║ 6         ║ "log"             ║ "/1/6/"   ║
║  8 ║ 6         ║ "lib"             ║ "/1/6/"   ║
╚════╩═══════════╩═══════════════════╩═══════════╝
In python you can use some ORM, such as sqlAlchemy, and, in that case, your folder would be represented as a class, implementing Model:
class Folder(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    parent_id = db.Column(db.Integer, db.ForeignKey('folder.id'),
        nullable=True)
    name = db.Column(db.String(128), unique=True, nullable=False)
    mpath = db.Column(db.String(255), unique=True, nullable=False)
Functionality to automatically create mpath value also could be placed in this class.