While both iptables -F and iptables -X perform cleanup operations, they target different aspects of iptables configuration:

# Flushes all rules in all chains (won't delete chains)
iptables -F

# Deletes all user-defined chains (only works when empty)
iptables -X

The sequence matters because you can't delete (-X) chains that contain rules. A common real-world scenario would be:

# Create custom chain
iptables -N MY_CHAIN

# Add rule to custom chain
iptables -A MY_CHAIN -j DROP

# This would FAIL because chain isn't empty
iptables -X MY_CHAIN

# Correct approach:
iptables -F MY_CHAIN  # First flush rules
iptables -X MY_CHAIN  # Then delete chain

When dealing with large rule sets, the order becomes particularly important for preventing memory leaks. The proper sequence ensures complete cleanup:

# Recommended cleanup procedure
iptables -F
iptables -X
iptables -Z  # Optional: zero counters

In automation scripts, it's wise to include error handling for chain deletion:

#!/bin/bash

# Flush all rules
iptables -F

# Delete user chains with error suppression
iptables -X 2>/dev/null || true

# Alternative for specific chain cleanup
if iptables -L CUSTOM_CHAIN &>/dev/null; then
    iptables -F CUSTOM_CHAIN
    iptables -X CUSTOM_CHAIN
fi

Built-in chains (INPUT, OUTPUT, FORWARD) can't be deleted with -X, but their policies remain after flushing:

# This will work (flush built-in chain)
iptables -F INPUT

# This will FAIL (can't delete built-in chain)
iptables -X INPUT

When working with iptables for Linux firewall management, two commonly used but distinct commands are:

iptables -F
iptables -X

The -F flag (or --flush) removes all rules from the selected chain. If no chain is specified, it flushes all chains in the table.

# Flush all rules in INPUT chain
iptables -F INPUT

# Flush ALL rules in ALL chains (default filter table)
iptables -F

The -X flag (or --delete-chain) deletes the specified user-defined chain(s). This command only works on empty chains (already flushed) and cannot delete built-in chains.

# Create a custom chain
iptables -N CUSTOM_CHAIN

# First flush any rules in it
iptables -F CUSTOM_CHAIN

# Then delete the chain
iptables -X CUSTOM_CHAIN

Typical cleanup sequence:

# Step 1: Remove all rules (including from custom chains)
iptables -F

# Step 2: Delete all empty user-defined chains
iptables -X

Imagine you've created a complex firewall setup with multiple custom chains:

iptables -N LOG_DROP
iptables -N PORT_SCAN_PROTECT
iptables -A INPUT -j PORT_SCAN_PROTECT
iptables -A PORT_SCAN_PROTECT -m recent --name ATTACKER --update --seconds 60 -j LOG_DROP

To properly clean this up:

# First flush all rules (including those jumping to custom chains)
iptables -F

# Then verify chains are empty
iptables -L

# Finally delete the custom chains
iptables -X LOG_DROP
iptables -X PORT_SCAN_PROTECT

• -F doesn't affect chain policies (ACCEPT/DROP)
• -X fails if chain contains rules or is referenced
• Built-in chains (INPUT, OUTPUT, FORWARD) cannot be deleted
• Always specify table (-t) when working with non-filter tables

For complex firewall resets including NAT rules:

# Flush and delete in all tables
for table in filter nat mangle raw security; do
    iptables -t $table -F
    iptables -t $table -X
done