Molecular nanotechnology requires computer-based design and analysis t
ools. Currently they are needed-as part of a computational approach to
nanotechnology-to allow detailed, analysed designs to be presented an
d discussed and to dovetail with efforts to develop fabrication capabi
lities. In the longer term, as fabrication capabilities emerge, they w
ill be needed for similar reasons as are needed in today's manufacturi
ng systems: to allow investigation of design alternatives and to contr
ol manufacturing systems. Given the huge number of 'parts' which may b
e required in molecular machines the need for computer-based tools wil
l, however, be even more primary for molecular nanotechnology than for
today's manufacturing technology, surpassing the CAD requirements of
VLSI. Whilst molecular CAD clearly shares some traits with existing CA
D, a fundamental difference is that the position and bonding of every
atom is of key interest in molecular manufacturing. This necessitates
new approaches and techniques. Molecular manufacturing will eventually
use diamondoid materials; materials which are crystalline. Molecular
CAD tools for the design of diamondoid structures must incorporate tec
hniques for manipulating crystalline materials. In this paper, we desc
ribe a molecular CAD tool-Crystal Clear-which allows the design of sim
ple diamondoid structures in full atomic detail using some novel techn
iques based on the crystalline nature of diamondoid materials.