In honor of Professor Paul Tseng, who went missing while on a kayak trip on the Jinsha river, China, on August 13, 2009, for his contributions to the theory and algorithms for large-scale optimization.Abstract. In this paper, we introduce a flexible optimization framework for nuclear norm minimization of matrices with linear structure, including Hankel, Toeplitz and moment structures, and catalog applications from diverse fields under this framework. We discuss various first-order methods for solving the resulting optimization problem, including alternating direction methods, proximal point algorithm and gradient projection methods. We perform computational experiments to compare these methods on system identification problem and system realization problem. For the system identification problem, the gradient projection method (accelerated by Nesterov's extrapolation techniques) usually outperforms other first-order methods in terms of CPU time on both real and simulated data; while for the system realization problem, the alternating direction method, as applied to a certain primal reformulation, usually outperforms other first-order methods in terms of CPU time.