atprogram -t avrispmk2 -i isp -d attiny13a chiperase
atprogram -t avrispmk2 -i isp -d attiny13a write -fs --values 6AF9
atprogram -t avrispmk2 -i isp -d attiny13a program -fl -f sce_v1.xx.hex
atprogram -t avrispmk2 -i isp -d attiny13a verify -fl -f sce_v1.xx.hex
atprogram -t avrispmk2 -i isp -d attiny13a write -lb --values FC

Answer	
Please find the following syntax for programming the fuse bytes in MegaAVR and TinyAVR with atprogram.exe tool.
atprogram.exe –t <tool> -i <interface> -d <device> write -fs --values <low_byte><high_byte><extended_byte>
 
For example
 
Atprogram.exe –t atmelice –i isp -d atmega328pb write -fs –values C2D9FF

Where the device ATmega328PB is programmed with following fuse values.
Low byte: C2
High Byte: D9
Extended Byte: FF