Eliminate 2 signals from 1 analog signal

[Shesha12345]

Thank you, sir, for giving me your understanding.

Actually I am using Atmega164A microcontroller and in coding I am generating a PWM of 3.125kHz frequency and I use Interrupt service routine for every rising edge my LED 750nm and 850nm working separately for every rising edge and for generating the signals I use DAQmx 6002 device to generate the signal and I use that signal in the interrupt service routine.
So, PWM and my control signal such as TRIG is combined together when LED glow and LOCK-In IC basically demodulate my signal.
So after demodulate I use a filter and in filter output, I have a combined signal of LED such as 750 and 850nm only.
Now I want to separate that signal individually such as 750nm and 850nm output show on a different graph chart.
I hope you understand my question.
If you need more clarification then please let me know.
Thank you so much.

[Henrik_Volkers]

I would rethink your stategy.

Start with a state maschine architekture

turn on one LED (blinking), let the lockin circuit do his work while capture AI for this LED

turn on other LED ...  

start with software timing

see how your system works ...   Lockin settle time? , improve timing

then start with sync DO and AI to get faster.  (you can use the PFI as a start trigger for your AI)

YOu want to do two seperate measurements, so treat them as two different signals.