If you create an Eloquent Model in Laravel (v.gr., the «Company» model), using the command
$ php artisan make:model Company
the file is stored in the «App» folder.
If you want to have all the model files into its own folder (v.gr., the «App/Models» folder), you have to create the folder
$ mkdir App/Models
Then you have to indicate all the route in the creation command
$ php artisan make:model Models/Company
Model created successfully.