You can remove trees, rocks and plants by: 

- Pressing once on the tree, rock or plant which you want to remove. 
- Drag the tool to the tree, rock or plant to remove. 
- If the tool count shows as 0 then you need to wait until you have collected the tool. 
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If you can not wait to collect the tool you need you can: 

- Buy the tool for the required amount of gems. 
- Head to the Social Market and see if another player is selling the tool.