Click on the tool to pick it up, then click on the item you want to harvest to harvest it. Your Harvests will then be sent to your Harvests & Products section of Storage You can find out all about the different sections of Storage in Chapter 14 - Storage To stop using the tool, click on the green man and the tool will be dropped. When you have finished harvesting and click the Walk icon (Green Man) to stop using the tool everything will come back into view.
If you can not see the crops trees or flowers that are on your farm, check your Preferences and make sure that on your farm, click on the Preferences icon and make sure that those items have check marks in the boxes. If you make any changes to your Preferences, make sure that you click on the green check mark at the bottom of the Preferences window to save those changes.