format pe console

 pushad
  mov ecx,[size]
  mov esi,[dat]
  lea edi,[esi+ecx]
  xor eax,eax
  @@:lodsb
     mov edx,eax
     mov ebx,eax
     and eax,7
     shr edx,3
     and edx,7
     shr ebx,6
     mov ah,byte[wct+eax]
     mov al,byte[wct+edx]
     shl eax,8
     mov al,byte[wct+ebx]
     mov [edi],eax
     add edi,3
  loop @b
  popad
.end start

dat dd ?
size dd ?     

It is not so simple. You need several things:

1. In order to read/write files in Windows you need to import needed functions from the Windows DLLs - You will need at least CreateFile ReadFile, WriteFile - Read the examples in FASM documentation, there is enough examples how the functions are imported.

2. In order to get the command line arguments (the filenames specified in your post) you will need the functions GetCommandLine and CommandLineToArgv

3. Read some more examples from FASM package. Download and read the help files about Win32 - there are described all Win32 functions you will need. As an alternative way - search for the function names in google - probably the first link will bring you to the description.

format pe gui 4.0

include 'win32ax.inc'
section '.code' executable
start:
        invoke CreateFile,fi,GENERIC_READ,NULL,NULL,\
               OPEN_EXISTING,FILE_ATTRIBUTE_NORMAL,NULL
               mov [hFile],eax

        invoke GetFileSize,[hFile],NULL
               mov esi,eax

        invoke CreateFile,fo,GENERIC_WRITE,NULL,NULL,\
               CREATE_NEW,FILE_ATTRIBUTE_NORMAL,NULL
               mov [hFout],eax

        invoke SetFileAttributes,fi,FILE_ATTRIBUTE_NORMAL
        invoke SetFileAttributes,fo,FILE_ATTRIBUTE_NORMAL
@@:
        invoke ReadFile,[hFile],lpBuffer,1,szReadByte,NULL
               inc [lpBuffer]
pushad
  mov ecx,[size]
  mov esi,[dat]
  lea edi,[esi+ecx]
  xor eax,eax
  @@:lodsb
     mov edx,eax
     mov ebx,eax
     and eax,7
     shr edx,3
     and edx,7
     shr ebx,6
     mov ah,byte[wct+eax]
     mov al,byte[wct+edx]
     shl eax,8
     mov al,byte[wct+ebx]
     mov [edi],eax
     add edi,3
  loop @b
size=$-dat ;$
  popad 
        invoke WriteFile,[hFout],lpBuffer,1,szFileWritten,NULL
               dec esi
               jnz @r

        invoke CloseHandle,[hFile]
        invoke CloseHandle,[hFout]

exit:
        invoke ExitProcess,NULL

.end start

section '.data' readable

        fi db 'i.txt',NULL
        fo db 'o.txt',NULL
        dat dd ?
wct db 'ABCDEFGO'
section '.data' readable writable

        hFile dd NULL
        szFile dd NULL
        lpBuffer dd NULL
        hFout dd NULL
        szFileWritten dd NULL
        szReadByte dd NULL    

format pe gui 4.0
entry start

include 'win32ax.inc'

section '.code' code readable executable

start:
        invoke CreateFile,"I.TXT",GENERIC_READ,NULL,NULL,OPEN_EXISTING,FILE_ATTRIBUTE_NORMAL,NULL
        mov [hInputFile],eax

        invoke GetFileSize,[hInputFile],NULL
        mov [dwFileSize],eax

        invoke LocalAlloc,LPTR,[dwFileSize]
        mov [lpBuffer],eax

        invoke ReadFile,[hInputFile],[lpBuffer],[dwFileSize],dwBytesRead,NULL

        invoke CloseHandle,[hInputFile]

;munge: ...

        invoke CreateFile,"O.TXT",GENERIC_WRITE,NULL,NULL,CREATE_ALWAYS,FILE_ATTRIBUTE_NORMAL,NULL
        mov [hOutputFile],eax

        invoke WriteFile,[hOutputFile],[lpBuffer],[dwFileSize],dwBytesWritten,NULL

        invoke CloseHandle,[hOutputFile]

        invoke LocalFree,[lpBuffer]

        invoke ExitProcess,NULL

section '.data' data readable writable

        hInputFile      dd 0
        hOutputFile     dd 0
        dwFileSize      dd 0
        dwBytesRead     dd 0
        dwBytesWritten  dd 0
        lpBuffer        dd 0

section '.idata' import data readable

 library kernel32,'KERNEL32.DLL',\
         user32,'USER32.DLL'

 include 'api\kernel32.inc'
 include 'api\user32.inc'    

        mov ecx,[dwFileSize]
        mov esi,[lpBuffer]
        mov edi,esi
munge:  lodsb
        xor al,MAGIC
        stosb
        loop munge