A wide range of dynamic systems can be approximated as linear and time invariant, for which a wealth of tools are available to characterize or modify their dynamic characteristics. Experimental modal analysis (EMA) is a procedure whereby the natural frequencies, damping ratios and mode shapes which parameterize vibratory, linear, time invariant systems are derived from experimentally measured response data. EMA is commonly applied in a multitude of applications, for example, to generate experimental models of dynamic systems, validate finite element models and to characterize dissipation in vibratory systems. Recent EMA has also been used to characterize damage or defects in a variety of systems. The Algorithm of Mode Isolation (AMI), presented by Drexel and Ginsberg in 2001, employs a unique strategy for modal parameter estimation in which modes are sequentially identified and subtracted from a set of FRFs. Their natural frequencies, damping ratios and mode vectors are then refined through an iterative procedure. This contrasts conventional multi-degree-of-freedom (MDOF) identification algorithms, most of which attempt to identify all of the modes of a system simultaneously. This dissertation presents a hybrid multi-input-multi-output (MIMO) implementation of the algorithm of mode isolation that improves the performance of AMI for systems with very close or weakly excited modes. The algorithmic steps are amenable to semi-automatic identification, and many FRFs can be processed efficiently and without concern for ill-conditioning, even when many modes are identified. The performance of the algorithm is demonstrated on noise contaminated analytical response data from two systems having close modes, one of which has localized modes while the other has globally responsive modes. The results are compared with other popular algorithms. MIMO-AMI is also applied to experimentally obtained data from shaker excited tests of the Z24 highway bridge, demonstrating the algorithm's performance on a data set typical of many EMA applications. Considerations for determining the number of modes active in the frequency band of interest are addressed, and the results obtained are compared to those found by other groups of researchers.