how do i clean my hamsters burrow if he retreats to it every time i get near his cage?

he sleeps in it too so that's not an option. if i want to see him i have to wait till he wakes up and go downstairs before he does and sit by the cage until he comes out. if i move too much he will retreat. i haven't checked that area yet (i got him pretty recently) so idk what's down there, if he pees there or not. he started coming out of it and going in a different way that's much more hidden so its harder to like see him coming in and out. it's almost been 3 months so it really need to check his burrow in case there's pee or rotten food. i don't want to have to dig him out because i don't want to have the first time i touch him be like that, he already isn't fond of me and doesn't want much to do with me so i feel like it'll make it worse. but im getting worried that's what ill need to do. plus i need to be able to handle him to take him to the vet. sorry this is long, im just anxious and i dont want him to get sick from a dirty burrow so i need to do this soon. any advice is appreciated.