Time-of-flight the secondary ion mass spectrometry (ToF-SIMS) is becoming a promising technique in analysis of a biological system due to its chemical specificity and the ability to perform high spatial resolution imaging. The combination of novel cluster and polyatomic beams has allowed generating images to map the distribution of biological components in tissue sections and cell surfaces. However, under these conditions the cluster beams have to be operated in the static regime, which limits sensitivity and confines the molecular imaging to 2 m spatial resolution. The polyatomic beams offer the benefits of high yields and low sub-surface damage, allowing the analysis to be performed at high ion fluence and abandoning the static limit. This presents a new approach to molecular imaging in which "voxels‟ are used rather than pixels, thus increasing sensitivity. As a result, the current SIMS instrumentation then becomes a limitation and has to be modified.A novel SIMS instrument, the J105 3D Chemical Imager has been developed with Ionoptika, which allows taking full advantage of the polyatomic primary beam, particularly the C60 by using it in a dc mode with buncher-ToF configuration. The aim of this project was to prove the concept and the potential of this new instrument.Initially standard organic samples have been used to show the current performance of the J105 for the analysis of organic samples with respect to a conventional ToF-SIMS instrument, the BioToF. The tandem MS capability of the instrument has been tested and proved using standard samples and a lipid mixture of brain extract.HeLa cells, an immortalised cell line were analysed using this instrument in 2D and 3D imaging mode. The images generated show molecular localisation on a sub-cellular scale, over a practical timeframe, whilst sustaining high mass resolution at 4000. The cells were imaged using a 40 keV C60+ dc beam and a clear differentiation between the material within the nuclei and lipid membrane can be made. Investigation of cell preparation suggested that the frozen-hydrated approach may be beneficial.The data presented in this thesis validates the new instrument concept offering the advantages of higher mass detection, increase in sensitivity, and an increase in the duty cycle while at the same time allowing imaging at sub-cellular scale with higher mass resolution.