Assumed mode methods are often used in vibrations analysis, where the choice of assumed mode affects the stability and useability of the method. System eigenfunctions are often used for these expansions, however a change in the boundary conditions usually results in a change in eigenfunction. This paper investigates the use of Alternative Admissible Functions (AAF) with penalties for the vibration analysis of an Euler-Bernoulli beam for different boundary conditions. A key advantage of the proposed approach is that the choice of AAF does not depend on the boundary conditions since the boundary conditions are modelled via penalty functions. The mathematical formulation of the system matrices, and the effect of beam geometry changes on the computed natural frequencies and modeshapes are presented. The computed natural frequencies and mode shapes show an excellent agreement when compared with closed-form Euler-Bernoulli beam values. The study reveals that with an increase in the stiffness of the beam, the values of the penalties need to be increased. The results of this study suggest that boundary conditions, as well as beam geometrical parameters should be considered when selecting appropriate values of the penalties.