Rabbits are creatures of habit and of association. It helps if things are familiar and if they have a pleasant association with it. You can work on this by putting the carrier in the room so she can walk in and out of it at will. You can also hide some treats in it to make it less of an “evil strange vet thing”, and more of a regular piece of furniture.
What also helps is trying to adjust her to being transported in it. I don’t know if you travel by car, but that also stresses out some rabbits. Taking her for a short drive regularly and using treats makes it a familiar and positive experience.
At the vet our Breintje often gets nervous in the waiting room. I usually take him out of his carrier and put him in my vest. It makes him feel safe and warm. We also bring a towel and an anti-slip mat to put on the exam table. Rabbits often hate the slippery table because they want to have a secure footing.
During the exam itself we keep talking to him and we occasionally pet him and use a “good boy” tone. We often bring a small treat such as a raisin to cheer him up. If he’s still very stressed afterwards he goes back in my vest for the journey home. Snug, warm and comfy. This is about as pleasant as we can make it.