Programming in binary would be ridiculous and insane, but yes it's possible to program using 64-bit binary opcodes for a 64-bit instruction set e.g Intel x64. It would never be a feasible choice though and even a simple hello world would take forever to write, 64-bit ASM which is the next step up from binary would be easier, but still very hardcore.
It's far more likely he's just compiling a program from a high level language like C# into a 64-bit executable binary, which is a simple compiler option. Writing 64-bit software is becoming more and more common.