How do I implement an FFT filter?

Just to preface this post, I am absolutely a beginner at coding with Arduino, so if anything in this sounds dumb or is a no brainer, cut me some slack xD

I'm designing an amp simulator for the Pedalshield Uno that passes the input signal through multiple gain stages, with each stage having it's own low and high pass filters, like a real amplifier meant for high levels of distortion.
There are a FFT libraries available to use of course, however, I find myself confused at how I would implement them into the ISR(TIMER1_CAPT_vect) timer interruptions that the example sketches use to read the input signal, modify it, then spit it back out.
Most of the examples of using FFT filters with Arduino that I've come across occur during the void loop() and involve Serial.print.
I'm aware that FFT filters would use up a lot of the Arduino's resources, I would just like to know how to implement them into the timer interrupts (if it's even possible).