How to create a control loop using a 100Msps digital signal as input
No Microprocessor is able to deal with such extreme rates as 100MS/s. That is clearly the domain of custom ICs and FPGAs, bringing the data to a very capable CPU, not something small and embedded.

Regarding USB:

I don't know your sampling bit width, but 40MB/s is not very much if you need to transport 100MS/s – you get 12bit per sample, in the ideal, zero-overhead case (which doesn't exist).

As a matter of fact, I know a series of devices very well that can deliver 100MS/s and more to a PC – these work through expensive interface such as a proprietary external PCIexpress interface, or better even through 10Gbit Ethernet (which you'd normally only find in data center / ISP equipment).

With a single 100MS/s stream you can easily flatten a single CPU core of a pretty capable x86_64 computer – really, that MUCH MUCH more data than what "microcontrollers" handle.

This might really be a case of insufficiently discussed system design – Nyquist and my understanding of the term "Ultrasound" say that you'd never need more than twice the highest signal frequency as sampling rate. I wouldn't expect ultrasound sonar to have frequencies higher than maybe 4 MHz, but I might be wrong.