How to filter a signal knowing the frequency response of a system in MATLAB?
Your signal is given by

$$x(t)=\sum_{1\le|k|\le 6}a_ke^{jk\omega_0t}\tag{1}$$

with $\omega_0=2\pi/T$.

An LTI system's response to $a_ke^{jk\omega_0t}$ simply is $H(jk\omega_0)a_ke^{jk\omega_0t}$, where $H(j\omega)$ is the system's frequency response. Consequently, the response to $x(t)$ is

$$y(t)=\sum_{1\le|k|\le 6}H(jk\omega_0)a_ke^{jk\omega_0t}\tag{2}$$

If you want to use Matlab, you could better use it to evaluate Eq. $(2)$, rather than to simulate the continuous-time system.