Imaging is powerful means of sample characterization where mineral abundances and surface areas can be quantified from mineral maps. Images are typically manually processed by domain experts, which is time-consuming, labor intensive, and subjective. Emerging techniques, such as machine learning based image processing, can potentially address these limitations and accelerate image processing but the performance of these models for accurate sample characterization and surface area analysis has not been completely evaluated. This study evaluates the potential of Random Forest and U-Net machine learning methods for mineral characterization and surface area analysis of six sandstone samples. Various input variable sets including filter extracted features, scanning electron microscopy (SEM) backscatter electron (BSE) images and SEM-energy dispersive x-ray spectroscopy images (EDS) images were considered. The evaluation was conducted by providing an intelligent framework that not only evaluates the accuracy of prediction for each pixel but also investigates the accuracy of predicted neighboring pixels. In addition, a new methodology is proposed to distinguish the more susceptible places to dissolution on the surface of a given mineral using a ranked mineral dissolution risk assessment map. The results showed both methods had an acceptable performance with the U-Net model outperforming Random Forest. Both methods showed an improved accuracy when filter extracted features were added to the dataset as input variables. The models’ performance predicting mineral abundances and accessibility agreed well with ground truth data for majority classes (e.g., quartz) compared to minority classes. Finally, the proposed methodology was shown to reliably identify the locations susceptible for dissolution indicated via proposed risk assessment maps. The intelligent segmentation and surface area analysis framework is a promising tool for accelerating the processing of SEM data and reactivity assessment of samples.