Hello house, are there nice/clean cars with manual transmission nowadays? Like Toyota Matrix or something like that. Lots of cars are now automatic transmission.
if there are, I'll appreciate pointers on where to find them. Thank you.

Them plenty nah, unfortunately the recent ones mostly comes in Nigerian used version especially the camry, Accord, sonata etc. But they have manual and are rear one in every 100 or so. You can try the 02-08 nissan primera, many peugot too out there are manual.

goodluck and welcome to the club

The only car I know (maybe those I cared to inquire sha) that doesn't have manual is Toyota sienna. Google any car you like, check its Wikipedia for its details, then, u be sure to find out your doubts.

Go to any reputable dealer and find out. Manual tranny of most common cars are available, but most dealers don't stock them because the demand for auto is incomparably higher.