I'm not sure when or how much to prune back my herbs. I have planted thyme, parsley, and basil in three small pots and I am worried the plants are crowding each other and not going to flourish. Should I thin these back? (look at the picture)
Planting Herbs Indoors
Certified GKH Gardening Expert
It does appear that you sowed the seeds great dense.
Generally the seed package give you specifics on how many seeds per inch in a planting tray.
When you sow seeds in large amounts in seeding trays or containers such as yours, you will need to 'prick' out the individual seedlings and place into individual pots.
This link will help you with this task.
I like to prick out and pot up my seedlings when they have at least 2 sets of true leaves.