The background should look something like this.
The 2 images are now aligned as 1.
Draw a square around the unwanted area...
...press "Delete" on the keyboard...
...and it's gone!
Use the mouse to find the best position for removal.
This will select the inverse of the model. Press "Delete" on the keyboard.
Rotate and zoom the model to make sure that it's clean.
It's also possible to remove multiple backgrounds at the same time. Just draw around what you would like to keep...
Now it's ready for alignment.
But it doesn't always work too well.
Don't worry though. You can still align the scans manually if that doesn't work.
This is an example of when it works well.
And here is the model all aligned with the background cleaned up and now ready for the next step.
Rotate it and zoom it to check it's beauty.
Save to "File..."
Choose the destination.
You can fix any holes with Meshmixer
Go to "Edit" and "Make Solid"
For more details on using Meshmixer, click on one of the buttons above.