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AVRdude

AVRDUDE is a command line tool to program AVR chips. It runs in the background of the Arduino IDE. Sometimes it is necessary to erase a chip or set the fuse bits that's when the AVRdude comes handy.

Dokumentations:
http://www.nongnu.org/avrdude/user-manual/avrdude.html
Command description:
http://www.nongnu.org/avrdude/user-manual/avrdude_4.html

-P
The device to which the programmer is attached is on
Linux: /dev/ttyACM0
Windows: com2
-c
The programmer for example: stk500v2

ATmega32U4
To erase the chip:

sudo avrdude -p m32u4 -c stk500v2 -P /dev/ttyACM0 -e -F

ATmega328p
To erase the chip:

sudo avrdude -p m328p -c stk500v2 -P /dev/ttyACM0 -e -F

ATmega168
set the fuse bits:

avrdude -c stk500v2 -p m168 -P /dev/ttyACM0 -B 6 -v -U lock:w:0x3f:m -U lfuse:w:0xff:m -U hfuse:w:0xdf:m -U efuse:w:0x0:m