For harvesting you can simply use the multi-tool and click on each square which is ready to harvest. You can also by the Harvester which can harvest 4 squares at a time.

You can also use the multi-tool to harvest individual animals and trees.

A milk barn is available which you can add up to 20 cows. You can click on this single barn and harvest all 20 cows at once.

A chicken coop is available which allows you to keep 20 chickens. You can click on this single coop and harvest all 20 chickens at once.