To assemble a source file you can use the either the m6811-elf-gcc driver or the m6811-elf-as program directly. Using the gcc driver is strongly recommended because gcc takes care of passing some important options.

68HC11
File type Command
GNU AS
m6811-elf-gcc -c -mshort -m68hc11 file.s
      
Motorola AS
m6811-elf-gcc -c -mshort -m68hc11 -Wa,--mri file.s
      
68HC12
GNU AS
m6811-elf-gcc -c -mshort -m68hc12 file.s
      
Motorola AS
m6811-elf-gcc -c -mshort -m68hc12 -Wa,--mri file.s
      

These commands will all produce an object file file.o in ELF format.