Linux Directory Structure and File System (Beginners to Pro Guide)

Introduction

Linux may seem intimidating at first, especially when you're greeted with folders like /etc, /var, /dev, and more. But once you understand the directory structure and file system hierarchy, navigating and managing your Linux system becomes much easier.

In the previous post we discussed Linux boot process and system workflow and in this post, we’ll break down the Linux File System Hierarchy Standard (FHS), explain what each major directory is for, and guide you through common commands used to explore the file system.

1.    What is the Linux File System?

2.    The Root Directory and File System Hierarchy

3.    File System Types in Linux

4.    Why Understanding the File System Matters

5.    What is File Permissions in Linux?

6.   How to change File Permissions Using chmod

7.   Special Permissions

8.   Security Tips

1. What is the Linux File System?

The Linux file system is a structured and standardized method of storing and organizing files on your Linux-based operating system. Unlike Windows, where drives like C:\ or D:\ represent partitions, Linux uses a single-rooted directory tree starting from / (called the root). Everything in Linux — files, directories, devices, and even processes — is treated as a file.

2. The Root Directory / and the File System Hierarchy

The top of the Linux file system is the root directory, denoted by /. All other files and directories stem from this root. Here's a breakdown of the most common directories you'll encounter.

2.1 / - Root Directory

This is the base of the file system. Every single file and directory starts from here.

2.2 /boot­­­­ Directory

This is one of the most important directories in the Linux file system. The boot directory contains Linux boot files as the bootloader, kernel and its related files. Image of Linux kernel stays here in the form of a compressed file.

2.3 /bin — Essential User Binaries

Contains basic Linux commands needed for system boot and recovery, available to all users.

2.4 /sbin — System Binaries

It is like a /bin directory but contains essential system binaries meant for root or administrative users.

2.5 /etc — Configuration Files

This directory holds system-wide configuration files and scripts used to initialize settings for programs and services.

2.6 /home — User Home Directories

Each user gets a personal folder under /home. This is where personal documents, downloads, and settings are stored.

2.7 /root — Root User’s Home Directory

This is the home directory of the root user, not to be confused with / (the file system root).

2.8 /var — Variable Files

Used for data that changes frequently, such as logs, spool files, caches, etc.

2.9 /usr — User System Resources

Contains read-only user applications, documentation, libraries, and binaries.

2.10 /tmp — Temporary Files

Temporary data used by applications or the system. Files are typically deleted after a reboot.

2.11 /dev — Device Files

Represents hardware devices like hard drives, terminals, USBs as files.

2.12 /proc and /sys — Virtual File system

These directories contain runtime system information, generated on-the-fly.

/proc includes process data and kernel parameters.

/sys exposes hardware information.

2.13 /lib — Essential Shared Libraries

Libraries required by binaries in /bin and /sbin. They’re similar to DLLs in Windows.

2.14 /media and /mnt — Mount Points

/media: automatically mounted removable devices (USB drives, CDs).

/mnt: used for manually mounting file systems or drives.

3. File System Types in Linux

Linux supports various file systems. Here are some common ones:

File System                       Description

Ext4                                  Default modern Linux file system; robust and fast

xfs                                    High-performance journaling file system

btrfs                                  Next-gen file system with snapshots and checksums

Vfat/fat32                          Used in USB drives and dual-boot environments

ntfs                                   Windows file system, supported via drivers

4. Why Understanding the File System Matters

·       Helps in troubleshooting system errors

·       Makes you confident using terminal-based tools

·       Crucial for Linux administration, DevOps and certification exams

·       Prevents accidental deletion of critical files

·       Helps in partitioning and backup strategies

5. What is File Permissions in Linux?

In Linux, everything is a file — whether it’s a document, a device, or a program. Each file or directory has permissions that define who can read, write, or execute that file.

These permissions are applied to three categories:

·       Owner – the user who owns the file

·       Group – a group of users assigned to the file

·       Others – everyone else

Types of Permissions

Symbol                  Permission            Description

r                              Read                       View file content or list directory

w                             Write                       Modify file content or directory files

x                              Execute                  Run file as a program or enter directory

File Permission Examples

1. -rwxr--r--

·       Owner: can read, write, and execute

·       Group: read-only

·       Others: read-only

2. drwxr-xr-x

·       Directory

·       Everyone can enter the directory

·       Only owner can modify contents

6. How to Change File Permissions Using chmod

The chmod command is used to change file modes or access permissions.

Symbolic Method

·       chmod u+x file.sh      # Add execute permission for user

·       chmod g-w file.sh      # Remove write permission for group

·       chmod o=r file.txt      # Set others to read-only

Numeric (Octal) Method

Each permission type has a value:

Permission  Value

·       Read (r)        4

·       Write (w)       2

·       Execute (x)   1

Directory Permissions

File permissions also apply to directories, but they work slightly differently:

Permission                       Effect on Directory

r                                        List contents of the directory

w                                       Create or delete files in the directory

x                                        Access files and subdirectories inside

7. Special Permissions

Set UID (s)

When set on executables, the program runs with the owner’s privileges, not the users.

·       chmod u+s program

Set GID (s)

When set on directories, new files inherit the group of the directory.

·       chmod g+s /data/shared

Sticky Bit (t)

Only the file owner or root can delete files in that directory.

Used commonly in /tmp:

·       chmod +t /tmp

8. Security Tips

·       Avoid giving 777 permissions — it gives full access to everyone

·       Use chmod -R cautiously — it applies changes recursively

·       Use groups to manage access to shared files

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