Minor scratches will happen, but generally they are easy to remove.
Depending on how deep the scratch is will dictate how much will come out. Using power buffers such as orbiting tools will ease the process but isn't required.
Apply a small amount of rubbing compound (maybe a dime size) to the edge of the foam buff.
Apply heavy pressure and buff in a circular motion to ensure complete coverage. Some will tell you not to buff in a circular motion.. This is false for rubbing compound.
Spend a good 5-10 minutes working on the area. Ease up on the pressure as you work into the scratch. It should start fading away as the grit particles in the compound start removing the top lair of the clear coat. Do not worry-- Most automobile paint jobs have 19mils of clear. Rubbing compound when applied with a power buffer will remove around 1-2mils per 10 minutes. By hand, maybe 1-2 per 20 minutes. You are in no danger of going through your paint.
