Laser cleaning of micron and sub-micron particles from various substrates such as silicon wafers and glass has been an active area of research in laser processing. Both understanding the fundamental physics of the light/particle/surface interaction and the development of successful cleaning protocols for industrial application have been drivers. It has been observed that directing the laser beam through a semi-transparent or transparent sample can give a higher laser cleaning efficiency for a given laser fluence than does front laser irradiation. In this work we present new comparative experimental results of “front and back” laser cleaning of silica particles from silica and glass substrates. Also, a comparison is made of the optical damage that occurs at higher laser fluences, beyond the damage free laser cleaning limit, for both.