Scanning electron microscopy (SEM) integrated with energy-dispersive X-ray spectrometry (EDS) are scientifically used to characterise the morphology, chemical composition and elemental distribution of powder samples. Upon an accessible analytical instrument, the specimen preparation method directly affects the quality and accuracy of the observation and analysis. In this paper, three preparation methods were utilised to characterise the carbon nanotubes (CNTs) based materials, and their strengths as well as the limitations are discussed. Thus, a characterisation strategy was established by comparing the obtained three measurement together with the derived sample information. To the end, we proposed to acquire the backscattered electron (BSE) images of nanoscale heavier nanoclusters grafted CNTs, typically for wide functional applications such as energy conversion and storage. Our proposed optimum method works particularly on the clarification of powder samples with small particle sizes and low atomic numbers, which underscores the involved contribution of SEM backscattered electron images.