Micro-expression recognition is a challenging task in computer vision field due to the repressed facial appearance and short duration. Previous work for micro-expression recognition have used hand-crafted features like LBP-TOP, Gabor filter and optical flow. This paper is the first work to explore the possible use of deep learning for micro-expression recognition task. Due to the lack of data for micro-expression, training a CNN model from micro-expression data is not feasible. Instead, transfer learning from objects and facial expressions based CNN models are used. The aim is to use feature selection to remove the irrelevant deep features for our task. This work extends evolutionary algorithms to search an optimal set of deep features so that it does not overfit the training data and generalizes well for the test data. Promising results are presented for various micro-expression datasets.