Is there a way to set all system processes other than my own process' threads to their own CPU without manually setting each pid.
I am using C on Fedora and would like to set this on program start not before.
cgroups (control groups) are an effective way of partitioning system resources (even more than just CPUs). Also, another effective way of getting exclusive CPU access for a process is to leverage the scheduler -- give it higher priority than anything else.
If those aren't what you want, and you've decided that you really, really want to control CPU affinity using single-bit masks, you can walk the process tree starting with init (try using system with this example of how to use ps at the shell).