There is a special cable called the x1541 cable that hooks a commodore floppy to a parallel printer port (I have such a cable, cost about $30, from some places online, or you can make your own, there are a few different versions, the most basic works mainly on older legacy machines (286, 386, 486, basic printer ports, DOS os) The more sophisticated ones work on ports that support EPP and ECP bi-directional transfers and newer OS's. I have one that is multi mode, not the best version, but not the basic either.
There is software that you can download free that will talk to the cable. CBM2DOS, I think is what it's called, I have it. It will run under Dos, Windows, WinXP, I haven't tried it in anything newer. Vice64 will interface with CBM2DOS, and be able to use the real drive just like you used it with the real C64.
There are other apps you can get that will allow you to image your floppies into D64 image files without even running the emulator.
I have archived my favorite floppies this way, I still have to use the cable to run my newsroom software, I haven't successfully gotten past the timing issues inherent to some copy protection algorithms that emulated disk images tend to have. (The copy protection on my original newsroom floppies are very timing dependent, literally looking for physical track position and tends to get scrambled in the emulated image, so the software won't load off the image, there are ways around it, I just haven't taken the time to crack it yet. I can successfully nibble the disk to another real floppy, just not to an image.)
Most my software is already cracked so it doesn't matter. That's the only program I haven't been able to image or find online. Games are easy to find and download, other apps for the 64 are a little harder to locate.
Anyways, yeah, just google commodore 64 x1541 cable. There is a wealth of info about it out there.
This is really the best source for info about it...
http://sta.c64.org/x1541.html