The Gcode program you used contains commands which set the height of the tool above the work surface. This may be in millimetres or inches, which depends on other Gcodes.
If you open up the Gcode file you used with a Text Editor, you will some lines contain instructions something like G00 Z3.000. This simply means "Move the Z-axis to 3.000 millimetres)" . It is possible for the number to be negative (e.g Z-3.000), in which case, if your zero point is level with the work surface, it will cut into it (take care!).
You can simply edit this 'Z' number so the tool is driven to the height you need. This command will appear throughout the Gcode file - you will need to check/modify all of them. Just change it to what you want, then save the file before using it.
Its also wise to make sure your machine is correctly zeroed before running the file. Camotics normally uses the bottom left corner when X= 0 and Y = 0, and if Z= 0, then the tool tip should be just touching the machine work surface - this depends to some extent on your machine how you do this.