The application of intrinsically conducting polymers (ICPs) for lab-on-chip applications has shown recent success with many research groups reporting novel methods to incorporate and control ICP materials in lab-on-chip platforms. Chemical and electrochemical polymerisation have been used to successfully incorporate ICP materials within microfluidic platforms. However, fabrication of 3D ordered flow-through ICP structures has remained a limitation in this research area to date. This work describes how fabricating a reproducible ICP templating method within the confines of a microfluidic channel consisting of a polystyrene (PS) sphere colloidal crystal (CC) provides a viable solution to this issue. The capillary force packing method developed as part of this thesis offers for the first time a quick and reliable method for the uniform fabrication of unimodal and bimodal CC templates in channel. This is in contrast to other methods such as drop casting, spin coating and dip-drawing which were designed for CC fabrication on planar substrates. Here, 3D ordered CC structures were fabricated exclusively within the µchannel which were ordered along the length, width and depth of the cuboid channel and CC thickness was dictated solely by µchannel depth. This is in contrast to other CC fabrication methods were volume fraction (VFS/L) dictates CC thickness. Subsequently, the CCs were utilised to template ICP materials, namely polyaniline (PANI), in a microfluidic channel, where PANI was grown via electrochemical polymerisation. It was shown that control of the electrochemical polymerisation time was critical not only to the depth of the resulting inverse opal PANI, but also to the intrinsic morphology and flow-through nature of the material. This research demonstrated the fabrication of significantly deeper PANI inverse opal structures than had been previously reported, due to the new CC templating method employed which could be achieve over a wide range of channel depths (e.g. 50 – 180 µm). Although, this increased channel depth resulted in an inherent inhomogeneity through the depth of the final electrochemically polymerised inverse opal structure due to a current density gradient. To overcome this inhomogenity, an investigation of chemical polymerisation of PANI was undertaken. Prior to CC template formation, aniline monomer was adsorbed onto the PS spheres in solution and subsequently packed in channel. After CC formation of aniline coated PS spheres, chemical polymerisation of the surface-confined aniline was carried out and templated PANI/PS opal structures were achieved. This chemical polymerisation method resulted in a 3D ordered, flow-through PANI/PS opal structures with homogeneous PANI coverage housed within a sealed microfluidic channel. By incorporation of a working electrode along the µchannel, the PANI structure was also electrochemically addressable maintaining the potential for lab-on-chip applications such sensing or separation. Finally the effect of dopant type on hydrophobicity of PANI films was investigated. Fabrication of PANI films was achieved on gold-sputtered working electrodes using HCl or Sodium dodecyl sulphate (SDS) as dopant. The PANI films were characterised by comparison of their water contact angle (WCA), morphology and surface roughness. It was found that SDS-doped PANI films displayed an ultra-hydrophobic WCA when doped, which upon dedoping became hydrophilic. In contrast, HCl-doped PANI films displayed hydrophilic surface chemistry with little variation upon doping/dedoping. When comparing surface roughness, SDS-doped PANI films displayed an order of magnitude higher roughness to that of the HCl-doped films, likely due to the soft templating effect of SDS during polymerisation. In summary this thesis presents new research into ICP structures that can be utilised to develop new applications in miniaturised platforms such as lab-on-chip. The benefits of the methods developed are the flow through nature and electrochemical addressability of the final ICP materials. In conjunction the templating method developed in this thesis offers a fabrication route for homogeneous 3D ordered ICP materials which are reproducibly templated in channel. The CC fabricated in this thesis offer a unique and versatile template for microfluidic applications where increased order or surface area is a requirement such as sensing and separation.