Unfortunately, Adam's suggestion won't work as his understanding of EBS is wrong (although I wish he was right and often thought myself it should work that way)... as EBS has nothing to do with S3, but it will only give you an "external drive" for EC2 instances that are separate, but connectable to the instances. You still have to do copying between S3 and EC2, even though there are no data transfer costs between the two.
You didn't mention an operating system of your instance, so I cannot give tailored information. A popular command line tool I use is http://s3tools.org/s3cmd ... it is based on Python and therefore, according to info on its website it should work on Win as well as Linux, although I use it ALL the time on Linux. You could easily whip up a quick script that uses its built in "sync" command that works similar to rsync, and have it triggered every time you're done processing your data. You could also use the recursive put and get commands to get and put data only when needed.
There are graphical tools like Cloudberry Pro that have some command line options for Windows too that you can setup schedule commands. http://s3tools.org/s3cmd is probably the easiest.