Creak hunting on a Fuel EXe is its own special kind of patience test, but the good news is the EXe has a fairly predictable list of usual suspects. Here's where I'd point the torch, roughly in order of likelihood:
1. The motor mount and covers
The TQ HPR50 sits in a tidy cradle, and like most mid-drives the bolts holding it can work loose and creak under pedalling load. On Trek bikes specifically, riders have traced "pedal hard and it creaks" noises to loose motor bracket bolts — caught early, thread-locking and re-torquing them sorts it.
@Zimmerframe has repeatedly flagged that motor bolt looseness is a primary creak source on e-bikes, and that just nipping up the cover alone only masks it:
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Worth a dab of carbon/assembly paste on the motor mount interface too — owners of the carbon Trek frames have found that quietens motor-area creaks.
2. Seatpost and saddle rails
The single most common creak on any bike, e or not. Drop the post, wipe the post and seat tube clean, and reinstall — carbon post gets assembly paste, alloy gets a light grease. Same with the saddle rail clamp. It's boring but it's free and it works more often than it has any right to.
3. Bottom bracket / cranks / pedals
A "click per pedal stroke" that's cyclical with your cadence is classic crank-interface or pedal-thread stuff. Pull the pedals, grease the threads, refit. Then check crank bolt torque.
4. Headset and through-axles
A creak that shows up out of the saddle, especially when pulling on the bars, is often the headset or a dry front axle. Clean and grease the axle and the headset bearing seats.
A useful diagnostic trick: creaks that are cyclical with
wheel rotation point at spokes or hub; creaks cyclical with
pedal rotation point at BB/cranks/motor; creaks that only happen when you load the bars point at headset/post. Isolating the rhythm narrows it down fast.
One thing I can't give you off the top of my head is the exact factory torque figures for the EXe's motor mount bolts — those are worth confirming against Trek's own spec sheet before you crank anything down, since over-torquing into a carbon frame is a worse problem than the creak.
If you can tell me
when the noise happens — pedalling vs coasting, seated vs standing, and whether it's in time with the pedals or the wheels — I can narrow it right down for you.