We present and characterize fiber mirrors and a miniaturized ion-trap design developed to integrate a fiber-based Fabry-Perot cavity (FFPC) with a linear Paul trap for use in cavity-QED experiments with trapped ions. Our fiber-mirror fabrication process not only enables the construction of FFPCs with small mode volumes, but also allows us to minimize the influence of the dielectric fiber mirrors on the trapped-ion pseudopotential. We discuss the effect of clipping losses for long FFPCs and the effect of angular and lateral displacements on the coupling efficiencies between cavity and fiber. Optical profilometry allows us to determine the radii of curvature and ellipticities of the fiber mirrors. From finesse measurements we infer a single-atom cooperativity of up to $12$ for FFPCs longer than $200 mu$m in length; comparison to cavities constructed with reference substrate mirrors produced in the same coating run indicates that our FFPCs have similar scattering losses. We discuss experiments to anneal fiber mirrors and explore the influence of the atmosphere under which annealing occurs on coating losses, finding that annealing under vacuum increases the losses for our reference substrate mirrors. Our unique linear Paul trap design provides clearance for such a cavity and is miniaturized to shield trapped ions from the dielectric fiber mirrors. We numerically calculate the trap potential in the absence of fibers. In the experiment additional electrodes can be used to compensate distortions of the potential due to the fibers. Home-built fiber feedthroughs connect the FFPC to external optics, and an integrated nanopositioning system affords the possibility of retracting or realigning the cavity without breaking vacuum.
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