In my game world, I have a Tree, that I've created in Blender:
However in my game world, I need to use over 50+ trees. So my question is, how do I reuse my Tree object without running into a messy Hierarchy like this:
It looks like something you've started doing already, but just to reaffirm your approach: you can create an empty GameObject (Create > Create Empty) named "Trees" and group your "Tree" objects under it.
In the event that this organization proves too broad, it could be a good idea to place your "Tree" objects under additional subgroups in "Trees", based on their location/purpose - for example, "HauntedForest", "StartingForest", etc.
Ultimately, what's most important is finding an organizational system that works for you, and staying consistent to it throughout your project.