Since 2004, when the Long Term Evolution (LTE) was first proposed to be publicly available in the year 2009, a plethora of new characteristics, techniques and applications have been constantly enhancing it since its first release, over the past decade. As a result, the research aims for LTE-Advanced (LTE-A) have been released to create a ubiquitous and supportive network for mobile users. The incorporation of heterogeneous networks (HetNets) has been proposed as one of the main enhancements of LTE-A systems over the existing LTE releases, by proposing the deployment of small-cell applications, such as femtocells, to provide more coverage and quality of service (QoS) within the network, whilst also reducing capital expenditure. These principal advantages can be obtained at the cost of new challenges such as inter-cell interference, which occurs when different network applications share the same frequency channel in the network. In this thesis, the main challenges of HetNets in LTE-A platform have been addressed and novel solutions are proposed by using self-organising network (SON) management approaches, which allows the cooperative cellular systems to observe, decide and amend their ongoing operation based on network conditions. The novel SON algorithms are modelled and simulated in OPNET modeler simulation software for the three processes of resource allocation, mobility management and interference coordination in multi-tier macro-femto networks. Different channel allocation methods based on cooperative transmission, frequency reuse and dynamic spectrum access are investigated and a novel SON sub-channel allocation method is proposed based on hybrid fractional frequency reuse (HFFR) scheme to provide dynamic resource allocation between macrocells and femtocells, while avoiding co-tier and cross-tier interference. Mobility management is also addressed as another important issue in HetNets, especially in hand-ins from macrocell to femtocell base stations. The existing research considers a limited number of methods for handover optimisation, such as signal strength and call admission control (CAC) to avoid unnecessary handovers, while our novel SON handover management method implements a comprehensive algorithm that performs sensing process, as well as resource availability and user residence checks to initiate the handover process at the optimal time. In addition to this, the novel femto over macro priority (FoMP) check in this process also gives the femtocell target nodes priority over the congested macrocells in order to improve the QoS at both the network tiers. Inter-cell interference, as the key challenge of HetNets, is also investigated by research on the existing time-domain, frequency-domain and power control methods. A novel SON interference mitigation algorithm is proposed, which is based on enhanced inter-cell interference coordination (eICIC) with power control process. The 3-phase power control algorithm contains signal to interference plus noise ratio (SINR) measurements, channel quality indicator (CQI) mapping and transmission power amendments to avoid the occurrence of interference due to the effects of high transmission power. The results of this research confirm that if heterogeneous systems are backed-up with SON management strategies, not only can improve the network capacity and QoS, but also the new network challenges such as inter-cell interference can also be mitigated in new releases of LTE-A network.