Facial micro-expressions, which usually last only for a fraction of a second, are challenging to detect by the human eye or machine. They are useful for understanding the genuine emotional state of a human face, and have various applications in education, medical, surveillance and legal sectors. Existing works on micro-expressions are focused on binary classification of the micro-expressions. However, detecting the micro-expression intensity changes over the spanning time, i.e., the micro-expression profiling, is not addressed in the literature. In this paper, we present a novel deep Convolutional Neural Network (CNN) based hybrid framework for micro-expression intensity change detection together with an image pre-processing technique. The two components of our hybrid framework, namely a micro-expression stage classifier, and an intensity estimator, are designed using a 3D and 2D shallow deep CNNs respectively. Moreover, we propose a fusion mechanism to improve the micro-expression intensity classification accuracy. Evaluation using the recent benchmark micro-expression datasets; CASME, CASME II and SAMM, demonstrates that our hybrid framework can accurately classify the various intensity levels of each micro-expression. Further, comparison with the state-of-the-art methods reveals the superiority of our hybrid approach in classifying the micro-expressions accurately.