Most of the existing tracking methods based on CNN(convolutional neural networks) are too slow for real-time application despite the excellent tracking precision compared with the traditional ones. Moreover, neural networks are memory intensive which will take up lots of hardware resources. In this paper, a feature selection visual tracking algorithm combining CNN based MDNet(Multi-Domain Network) and RoIAlign was developed. We find that there is a lot of redundancy in feature maps from convolutional layers. So valid feature maps are selected by mutual information and others are abandoned which can reduce the complexity and computation of the network and do not affect the precision. The major problem of MDNet also lies in the time efficiency. Considering the computational complexity of MDNet is mainly caused by the large amount of convolution operations and fine-tuning of the network during tracking, a RoIAlign layer which could conduct the convolution over the whole image instead of each RoI is added to accelerate the convolution and a new strategy of fine-tuning the fully-connected layers is used to accelerate the update. With RoIAlign employed, the computation speed has been increased and it shows greater precision than RoIPool. Because RoIAlign can process float number coordinates by bilinear interpolation. These strategies can accelerate the processing, reduce the complexity with very low impact on precision and it can run at around 10 fps(while the speed of MDNet is about 1 fps). The proposed algorithm has been evaluated on a benchmark: OTB100, on which high precision and speed have been obtained.