Automatic detection of corrosion and associated damages to civil infrastructures such as bridges, buildings, and roads, from aerial images captured by an Unmanned Aerial Vehicle (UAV), helps one to overcome the challenges and shortcomings (objectivity and reliability) associated with the manual inspection methods. Deep learning methods have been widely reported in the literature for civil infrastructure corrosion detection. Among them, convolutional neural networks (CNNs) display promising applicability for the automatic detection of image features less affected by image noises. Therefore, in the current study, we propose a modified version of deep hierarchical CNN architecture, based on 16 convolution layers and cycle generative adversarial network (CycleGAN), to predict pixel-wise segmentation in an end-to-end manner using the images of Bolte Bridge and sky rail areas in Victoria (Melbourne). The convolutedly designed model network proposed in the study is based on learning and aggregation of multi-scale and multilevel features while moving from the low convolutional layers to the high-level layers, thus reducing the consistency loss in images due to the inclusion of CycleGAN. The standard approaches only use the last convolutional layer, but our proposed architecture differs from these approaches and uses multiple layers. Moreover, we have used guided filtering and Conditional Random Fields (CRFs) methods to refine the prediction results. Additionally, the effectiveness of the proposed architecture was assessed using benchmarking data of 600 images of civil infrastructure. Overall, the results show that the deep hierarchical CNN architecture based on 16 convolution layers produced advanced performances when evaluated for different methods, including the baseline, PSPNet, DeepLab, and SegNet. Overall, the extended method displayed the Global Accuracy (GA); Class Average Accuracy (CAC); mean Intersection Of the Union (IOU); Precision (P); Recall (R); and F-score values of 0.989, 0.931, 0.878, 0.849, 0.818 and 0.833, respectively.