files, temp files, and file-like objects

[gyromagnetic]

Hi,
I am building an application in which many of the properties of
objects are computed based on results produced by a number of external
applications. Each of these compiled (C or Fortran) applications is
usually run from the command line with a generic syntax like
   command -i input file -o outputfile_basename

In the process of 'doing their stuff', each application creates a slew
of temporary and subsidiary output files. My objects' properties
(numbers) are usually taken from one or two of the output files, while
the rest of the files are 'clutter' for my purposes.

My question is 'how should I handle the many, many files that are
involved?'
I will be creating hundreds of objects, with each one potentially
creating a dozen files in the process. Is there some kind of file-like
objects that can be used instead of real files that could 'fool' the
applications?

I would appreciate any suggestions that you can give me.

Thanks.

-gyro