Clandestine means kept secret or done secretively, another way of saying hidden. So a clandestine grave is one that's hidden, not one that is easily seen/marked in a graveyard. An example of a clandestine grave might be that of a homicide victim buried in the woods where no one is likely to find it.
Because the grave is hidden, geophysics (involving the use of a variety of electromagnetic techniques) can be used to outline, discover, and plan an exhumation including ground-penetrating radar (GPR), terrain conductivity (EM), thermal infrared (IR) imagery, as well as magnetometers and metal detectors.
Frequently, when the potential location of a clandestine grave is determined, the first impulse by investigators is to start digging, often with a backhoe. Get more details here.
In the news, 44 victims of the violence committed by the Mara Salvatrucha (MS-13) and Barrio 18 gangs have been found in mass graves in a dense forest in the municipality of Colón, 20 kilometers west of San Salvador. Read more at Infosurhoy.